Download snp file

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Snp File Reader, free snp file reader software downloads, Page 3.

SNP file extension - What is SNP file? How to open SNP files?

SNP Analyser was developed as an easy-to-use and useful utility for the efficient analysis and management of Affymetrix SNP DMET Data analysis. SNP Analyser is a software that was designed with the help of the Java programming language.File Name:SNP_Analyser1.1.4.jar Author:Peppe, Pietro Hiram GuzziLicense:Freeware (Free)File Size:Runs on:Windows All Advertisement Advertisement GSA-SNP is a gene set analysis software that can process SNP data as well as gene and haplotype GSA-SNP is a gene set analysis software that can process SNP data as well as gene and haplotype data..File Name:GSA-SNP.jar Author:gsa-snpLicense:Freeware (Free)File Size:247 KbRuns on:Windows; LinuxReports the difference between different SNP values in terms of Transcription Binding Reports the difference between different SNP values in terms of Transcription Binding efficiencies..File Name:Get_SNP_Info.jar Author:snpscoreLicense:Freeware (Free)File Size:5 KbRuns on:N/ASNPTools is a suite of tools that enables integrative SNP analysis in next generation sequencing data with large cohorts. It not only calls SNP in a population with high sensitivity and accuracy, but also employs a novel imputation engine to achieve ...File Name:snptools-1.0.tar.gz Author:Danny Challis, Fuli Yu, JinYu, Yi Wang, Zhuoyi HuangLicense:Freeware (Free)File Size:508 KbRuns on:BSD; LinuxThe annotation files for Illumina SNP genotyping platforms generated for performing Homozygosity Haplotype The annotation files for Illumina SNP genotyping platforms generated for performing Homozygosity Haplotype analysis.File Name:HH annotations for IlluminaSNP chip Author:hhannotLicense:Freeware (Free)File Size:26.21 MbRuns on:Windows; Mac; LinuxThis software detects homologous horizontal gene transfer (HGT) from SNP data. Based on SNP alleles calls and locations, it breaks the genomes into locally colinear blocks, and looks for cases where SNPs do not agree with the vertical pattern of ...File Name:HGT_paper_data.zip Author:Shea GardnerLicense:Freeware (Free)File Size:888.52 MbRuns on:BSD; LinuxCNViewer is designed to allow the visual comparison of copy number (CN state) and loss of heterozygosity (LOH) data from Affymetrix SNP 6.0 microarrays between affected and unaffected members of a pedigree. The program aims to Allow the identification ...File Name:CNViewer Author:dna.leeds.ac.ukLicense:Freeware (Free)File Size:Runs on:WindowsEasy Homozygosity Profiling of Affymetrix SNP Easy Homozygosity Profiling of Affymetrix SNP Arrays.File Name:CMT_R.zip Author:ehopasaLicense:Freeware (Free)File Size:4 KbRuns on:Windows; LinuxReader is the ultimate Reader tool that . Reader is the ultimate Reader tool that brings the Safari 5 Reader features to Firefox and helps you read more of the web by transforming text on any website using fonts, colors, and layouts of your choosing..File Name:reader-0.4-fx.xpi Author:Baris DerinLicense:Freeware (Free)File Size:92 KbRuns on:LinuxAssist you to read PDF freely and digitally sign and print all PDF files. Tipard Free PDF Reader is your best assistant to read PDF file. With this PDF Reader, you can open, view, zoom and print all PDF documents freely.File Name:Tipard Free PDF Reader Author:Tipard StudioLicense:Shareware ($)File Size:8.19 MbRuns on:WinXP, WinNT 4.x, Win2003, Win2000, Win Vista, Windows 7, Windows 7 x64This is a Perl module for doing snp analysis based on shotgun sequencing reads and a reference genome sequence. Its primary input is the cigar alignment format outputted from ssaha2..File Name:SNP/Indel Analysis Author:Jacqui, ThomasLicense:Freeware (Free)File Size:Runs on:WindowsCurrently GEDI-ADMX handles genotype data from unrelated individuals.Local ancestry inference uses a factorial HMMs trained on ancestralhaplotypes to impute genotypes at all typed SNP loci (temporarily markingeach SNP genotype as missing) under each possible local ancestry.GEDI-ADMX assigns to each locus the local ancestry that yields the highestimputation accuracy, as assessed using a weighted-voting scheme based onmultiple SNP windows .File Name:GEDI-ADMXViewer-1.0.3.zip Author:Bioinformatics LabLicense:Freeware (Free)File Size:7.34 MbRuns on:Win All

.SNP - How to open SNP file? SNP File Extension - FileInfo

Is for a SNP or location based on the reference sequence (HG38).Genotype - This lists what your value )A, C, T, or G) is for a SNP or location compared to the reference sequence (HG38).Download VCFFor the advanced user, we have made the BigY raw data files available for download. The download will be a zipped archive that contains a VCF and a BED file.The VCF file contains a list of all variants found using the build 38 human genome reference. You can find more info about the VCF file format here.We include variants that did not pass our analysis standards for your informational purposes only.The BED file contains the regions that were targeted in Big Y and passed our sequencing and analysis quality control. You can find more info about the BED file format here.Buy Raw DataYour Big Y data can be compiled into a BAM file. This entails an additional internal cost to convert, store, and provide this large file format. Originally this price was included in the cost of the Big Y test and was available to download when results were complete. However, only a small portion of Big Y participants request this download. Rather than continue to pass this cost along to all Big Y participants, we have chosen to only charge those who wish to download their BAM file for that data. You can read more about BAM files here. Was this article helpful? Yes No -->. Snp File Reader, free snp file reader software downloads, Page 3.

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File. The picture does NOT include the softkeys. Data (csv) Saves trace data from the current Mode to a *.csv file. This format can be imported into spreadsheet software such as Microsoft Excel. Column A is always the frequency at which the data is measured. In SA Mode, all visible data traces are saved. Each trace is saved to a separate column that is labeled with the Trace State. In CAT and NA Modes, only the data trace is saved – not the memory trace. In Power Meter (with Option 208 Frequency Offset Power Sensor (FOPS)), all visible traces are saved. Each trace is saved to a separate column labeled Output Power or Memory. In VVM Mode, NO data is saved. Group Saves a group of file types that have been selected in the Preferences menu. Learn more, see “Group Save File Types Editing”. Data (S1P) / (S2P) Saves CAT and NA Mode trace data to an *.S1P or *.S2P file, depending on the active measurement. This file format is used by CAE programs such as Keysight's Microwave Design System (MDS) and Advanced Design System (ADS). It can also be imported into spreadsheet software such as Microsoft Excel.About SNP FilesThe SNP file includes header information, and the following data: S1P - saves 1-port (receiver) data for the active data trace. *.s1p Files contain 1 stimulus value and 1 S-parameter (total of 3 scalar values) Stim Real(Sxx) Imag(Sxx) S2P (NA Mode ONLY) - saves 2-port data for the active trace. *.s2p Files contain 1 stimulus value and 4 S-parameters (total of 9 scalar values) Stim Real(S11) Imag(S11) Real(S21) Imag(S21) Real(S12) Imag(S12) Real(S22) Imag(S22) Only data traces are saved – not memory traces.Corrections When parameters are corrected, data is returned even when not displayed. Data is returned with the correction type that is applied for each S-parameter. The correction type for each S-parameter is annotated in the header. When parameters are NOT corrected or displayed: With Smith chart and Polar formats, Real/Imag zero-filled data appears as (1.0, 0.0). With all other formats, LogMag/Phase zero-filled data appears as (0.0, 0.0). > Display formatsIn CAT Mode, S1P files are always Magnitude (dB) / Phase (angle) format.In NA Mode: Smith chart and Polar display formats are ALWAYS saved in Real/Imag data pairs. All other display formats are saved in LogMag/Phase (dbAngle).> What Data Processing functions are included in saved SNP Data:In NA Mode, the data processing functions (such as trace math) that are included in the SNP data depends on a Preference setting. Click System, then Preferences, then Preferences, then scroll to NA, SNP File Save, then select from the following: Default – SNP data does NOT include smoothing. SNP data saves are taken AFTER data processing (location 2) on the processing chain. Advanced – SNP data includes the following: With Smith or Polar display format, SNP data saves are taken BEFORE most processing (location 1 on the data processing chain). With any other display format, SNP data saves are taken just AFTER Formatting and The same reference, you canproduce an alignment of "core SNPs" which can be used to build ahigh-resolution phylogeny (ignoring possible recombination). A "core site"is a genomic position that is present in all the samples. A core site canhave the same nucleotide in every sample ("monomorphic") or some samples canbe different ("polymorphic" or "variant"). If we ignore the complicationsof "ins", "del" variant types, and just use variant sites, these are the "core SNP genome".Input Requirementsa set of Snippy folders which used the same --ref sequence.Using snippy-multiTo simplify running a set of isolate sequences (reads or contigs)against the same reference, you can use the snippy-multi script.This script requires a tab separated input file as follows, andcan handle paired-end reads, single-end reads, and assembled contigs.# input.tab = ID R1 [R2]Isolate1 /path/to/R1.fq.gz /path/to/R2.fq.gzIsolate1b /path/to/R1.fastq.gz /path/to/R2.fastq.gzIsolate1c /path/to/R1.fa /path/to/R2.fa# single end reads supported tooIsolate2 /path/to/SE.fq.gzIsolate2b /path/to/iontorrent.fastq# or already assembled contigs if you don't have readsIsolate3 /path/to/contigs.faIsolate3b /path/to/reference.fna.gzThen one would run this to generate the output script.The first parameter should be the input.tab file.The remaining parameters should be any remainingshared snippy parameters. The ID will be used foreach isolate's --outdir. runme.sh% less runme.sh # check the script makes sense% sh ./runme.sh # leave it running over lunch">% snippy-multi input.tab --ref Reference.gbk --cpus 16 > runme.sh% less runme.sh # check the script makes sense% sh ./runme.sh # leave it running over lunchIt will also run snippy-core at the end to generate thecore genome SNP alignment files core.*.Output FilesExtensionDescription.alnA core SNP alignment in the --aformat format (default FASTA).full.alnA whole genome SNP alignment (includes invariant sites).tabTab-separated columnar list of core SNP sites with alleles but NO annotations.vcfMulti-sample VCF file with genotype GT tags for all discovered alleles.txtTab-separated columnar list of alignment/core-size statistics.ref.faFASTA version/copy of the --ref.self_mask.bedBED file generated if --mask auto is used.Why is core.full.aln an alphabet soup?The core.full.aln file

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SNP File: How to open SNP file (and what it is)

To your system. Manual : Specify the time manually. Synchronize with NTP server : Sync with the time of the specified server address. Synchronize with PC viewer : Synchronize the time with the connected PC. When done, click [Apply ( ... Page 93 Upgrade / Reboot From the Setup menu, select the tab. Click . Select a desired item and set it appropriately. • Upgrade : Performs upgrading the system. • Factory default : Resets the system to the factory default. Except network parameter : Reset the other settings except for the interface/port/DDNS/IP filtering settings. Page 94 setup screen To save the current settings and restore the backup settings Click [Backup]. The Save As dialog should appear. Specify the backup path with a proper file name, and click [Save]. The backup file will be saved to the specified path in the format of “.bin”. Page 95 From the right log list, select an item to search for. • If you select in the top left dropdown list, all logs for the applicable log type will be displayed. If one page can not display all the logs available, use the bottom buttons to move to the previous, next, or the last item. Page 96: Appendix appendix appendix SPECIFICATION Description Items SNP-5200N/P SNP-5200HN/HP Imaging Device 1/3" 1.3M PS CMOS Total Pixels 1,384(H) x 1,076(V) Effective Pixels 1,329(H) x 1,049(V) Scanning System Progressive Video Color : 0.7 Lux (F1.6, 50IRE), 0.01Lux (Sens-up 60X, 50IRE) Min. Illumination B/W : 0.08 Lux (F1.6, 50IRE), 0.001Lux (Sens-up 60X, 50IRE) S / N Ratio 52dB Video Out... Page 97 Auto (ICR) / Color / B/W Backlight Compensation Off / BLC / HLC Wide Dynamic Range Contrast Enhancement SSDR (Samsung Super Dynamic Range) (Off / On) Digital Noise Reduction SSNRIII (2D+3D Noise Filter) (Off / On) Digital Image Stabilization Off / On... Page 98 Intelligent Video Analytics Appear / Disappear Operational Alarm I/O Input 4ea / Output 2ea (Relay) Remote Control Interface RS-485/422 SAMSUNG-T/E, PELCO-P/D, Panasonic, Honeywell, AD, RS-485 Protocol Bosch, Vicon, GE Ethernet RJ-45 (10/100BASE-T) Video Compression Format H.264, MPEG-4, MJPEG 1280x1024, 1280x720P(HD), 1024x768, 800x600,... Page 99 Description Items SNP-5200N/P SNP-5200HN/HP HTTPS(SSL) Login Authentication Digest Login Authentication Security IP Address Filtering User access Log 802.1x Authentication Streaming Method Unicast / Multicast Max. User Access 10 users at Unicast Mode Memory Slot SD/SDHC Memory Slot Network ONVIF Conformance English, French, German, Spanish, Italian, Chinese, Korean, Russian, Japanese, Swedish, Denish, Portuguese, Czech, Webpage Language... Page 100: Product Overview PRODUCT OVERVIEW ❖ SNP-5200 Ø155 100_ appendix... Page 101 ❖ SNP-5200H Ø248 Ø244 Ø148 Ø162 English _101... Page 102: Troubleshooting appendix TROUBLESHOOTING PROBLEM SOLUTION Check to make sure that the camera’s Network settings are appropriate. Check to make sure that all. Snp File Reader, free snp file reader software downloads, Page 3. What is a SNP file? Learn about the file formats using this extension and how to open SNP files. Download a SNP opener. Learn from the File Experts at file.org.

SNP File Extension - What is it? How to open an SNP file?

The sequence, counting from 1TYPEThe variant type: snp msp ins del complexREFThe nucleotide(s) in the referenceALTThe alternate nucleotide(s) supported by the readsEVIDENCEFrequency counts for REF and ALTIf you supply a Genbank file as the --reference rather than a FASTAfile, Snippy will fill in these extra columns by using the genome annotationto tell you which feature was affected by the variant:NameDescriptionFTYPEClass of feature affected: CDS tRNA rRNA ...STRANDStrand the feature was on: + - .NT_POSNucleotide position of the variant withinthe feature / Length in ntAA_POSResidue position / Length in aa (only if FTYPE is CDS)LOCUS_TAGThe /locus_tag of the feature (if it existed)GENEThe /gene tag of the feature (if it existed)PRODUCTThe /product tag of the feature (if it existed)EFFECTThe snpEff annotated consequence of this variant (ANN tag in .vcf)Columns in TXT formatNameDescriptionIDReference + SampleLENGTHLength of the referenceALIGNEDNumber of sites aligned toUNALIGNEDNumber of sites unalignedVARIANTNumber of sites different from the referenceHETNumber of sites heterozygous or poor quality genotype represented with an n (--minqual)MASKEDNumber of sites masked in reference represented with an X (--mask)LOWCOVNumber of sites low coverage in this sample represented with an N (--mincov)Variant TypesTypeNameExamplesnpSingle Nucleotide PolymorphismA => TmnpMultiple Nuclotide PolymorphismGC => ATinsInsertionATT => AGTTdelDeletionACGG => ACGcomplexCombination of snp/mnpATTC => GTTAThe variant callerThe variant calling is done byFreebayes.The key parameters under user control are:--mincov - the minimum number of reads covering a site to be considered (default=10)--minfrac - the minimum proportion of those reads which must differ from the reference--minqual - the minimum VCF variant call "quality" (default=100)Looking at variants in detail with snippy-vcf_reportIf you run Snippy with the --report option it will automatically runsnippy-vcf_report and generate a snps.report.txt which has a sectionlike this for each SNP in snps.vcf:LBB_contig000001:10332 snp A=>T DP=7 Q=66.3052 [7] 10301 10311 10321 10331 10341 10351 10361tcttctccgagaagggaatataatttaaaaaaattcttaaataattcccttccctcccgttataaaaattcttcgcttat........................................T.......................................,,,,,, ,,,,,,,,,,,,,,,,,,,,,t,,,,,,,,,,t,,t,,,,,,,,,,,,,,,,g,,,,,,,g,,,,,,,,,t,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, .......T..................A............A................................A........A.....T........... .........C...................A.....................C..C........CT.................TA.............,a,,,,,a,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,t,t,,,g,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,ga,,,,,,,c,,,,,,,t,,,,,,,,,,g,,,,,,t,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, ............T.C..............G...............G...... ,,,,,,,g,,,,,,,,g,,,,,,,,,,, g,,,,,,,,,,,,,,,,,,,,">~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~>LBB_contig000001:10332 snp A=>T DP=7 Q=66.3052 [7]