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<prev • 252 results • page 1 of 9 • next >
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Invalid BAI magic number - TorrentVariantCaller
variant calling written 2.4 years ago by A Soggy Waffle • 0 • updated 2 days ago by kmzhou4 • 0
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Example code of MCMC on somatic variant calling (site specific error model)
variant calling written 24 days ago by CY • 480
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Evaluating RMSMappingQuality profile to set threshold
variant calling gatk snp filtering written 5 weeks ago by serpalma.v • 40 • updated 5 weeks ago by Nicolas Rosewick ♦ 8.8k
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140
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Calling chrMT only from BAM
variant calling assembly mt written 3 months ago by igorm • 10
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114
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[bcftools] [linux cluster] subset vcf.gz file per snp keeping headers and columns
variant calling software error bcftools snp written 8 weeks ago by mgois • 0 • updated 8 weeks ago by arnstrm • 1.8k
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120
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allele frequency bcf tools
variant calling snp written 8 weeks ago by jh • 20 • updated 8 weeks ago by Kevin Blighe ♦ 61k
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How can I input a BAM file to the samtools mpileup command without using a text file?
variant calling bam samtools mpileup written 3.4 years ago by cristian • 240 • updated 8 weeks ago by Biostar ♦♦ 20
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96
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Freebayes adjusting parameters to "force" homozygous call
variant calling freebayes written 4 months ago by User000 • 380 • updated 8 weeks ago by Biostar ♦♦ 20
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Suggested pipeline to perform variant calling for cancer exome sequencing samples of PDX models
variant calling pdx wes liquid biopsy written 5 months ago by svlachavas • 680 • updated 10 weeks ago by akshayb04 • 20
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Fatal error reading file snpEff.config with SnpEff
variant calling snpeff fatal error written 12 weeks ago by aguiller.mateos • 0
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14 follow
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Tool: ClinCNV: CNV detection from short reads
cna variant calling tool cnv written 8 months ago by German.M.Demidov • 1.7k
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Pisces and Octopus on WES
variant calling pisces wes octopus written 3 months ago by newbio17 • 110
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8 follow
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Tool: Arriba: Fast and accurate gene fusion detection from RNA-Seq data
variant calling tool cancer fusion rna-seq gene written 2.4 years ago by uhrigs • 100 • updated 3 months ago by gratefulheart946 • 0
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191
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Problems in Variant Calling Code
variant calling snp written 3 months ago by arjun.murthy779 • 10
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120
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Reference of Whole exome sequecing analysis
variant calling ngs wes mutation bwa written 3 months ago by Shahzad • 10 • updated 3 months ago by lakhujanivijay ♦ 5.1k
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GATK's NuMT detection algorithm?
variant calling gatk mitochondria written 5 months ago by a.j.wilson0000 • 10 • updated 3 months ago by Biostar ♦♦ 20
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125
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Variant calling on aligned BAM files of WES
variant calling rna-seq written 4 months ago by atheeth14 • 0 • updated 4 months ago by genomax ♦ 85k
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1
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Somatic variant calling with/without matched normal sample (Mutect2)
variant calling gatk wes mutect2 written 4 months ago by newbio17 • 110 • updated 4 months ago by markus.riester • 490
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165
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Difference between HISAT2 grch38 and grch38_snp indexes
variant calling exome alignment snp hisat2 written 4 months ago by ScubaChris • 10
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153
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HaplotypeCaller: java.lang.NullPointerException when multiple-line bed file is used
variant calling gatk written 4 months ago by godth13teen • 20 • updated 4 months ago by Pierre Lindenbaum ♦ 129k
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Assigning separate samples to groups in a vcf file
variant calling snp written 4 months ago by evolozzy • 10
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5 follow
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Are there any issues with using sample reads coming from different technologies and having different depths to do joint variant calling (gatk)?
variant calling gatk hiseq snp novaseq written 4 months ago by serpalma.v • 40 • updated 4 months ago by bari.ballew • 220
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116
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VCF quality indicators
variant calling next-gen wes snp normal-tumor written 4 months ago by Martina • 30
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Which of the 4 SureSelect Agilent BED files to use with GATK haplotype caller?
variant calling gatk sureselect written 4 months ago by curious • 320
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How to determine which bam/sam lines correspond to called structural variant using Freebayes
variant calling freebayes snp written 4 months ago by mdriskil • 10
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find variants compared to sequenced reference in coding sequences
variant calling written 5 months ago by nibhelim • 0
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News: Live webinar (Feb 12 at 12PM Eastern): variant calling for bench scientists
variant calling tutorial wes wgs news software tools written 5 months ago by Basepair • 0 • updated 5 months ago by h.mon ♦ 30k
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1
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Split BAM file from paired end read into forward and reverse strand w.r.t reference genome
variant calling ngs samtools rna-seq snp written 5 months ago by Susmita Mandal • 60 • updated 5 months ago by ATpoint ♦ 36k
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Tools and/or methods to detect allelic mapping bias.
variant calling ngs rna-seq snp alelle specific written 5 months ago by Susmita Mandal • 60
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What is the difference between mpileup samtools and bcftools?
variant calling bcftools samtools mpileup snp written 5 months ago by beausoleilmo • 310 • updated 5 months ago by jkbonfield • 390
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