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<prev • 106 results • page 1 of 4 • next >
0
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3
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161
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3
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How to make variant calling run faster?
variant calling gatk mutect2 written 4 days ago by steve • 890 • updated 4 days ago by Brian Bushnell ♦ 14k
10
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3
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322
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6 follow
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DNA sequence of genes from vcf file
vcf variant calling bcftools gene ensembl written 11 weeks ago by bioinfo8 • 90 • updated 4 days ago by songbaoxing168 • 0
2
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0
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152
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0
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Detecting gene insertions with DiscoSNP
variant calling discosnp written 7 weeks ago by laeb • 60 • updated 19 days ago by Biostar ♦♦ 20
2
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1
answer
180
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1
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What does ALT 0 mean in a VCF?
variant calling sequence alignment written 5 weeks ago by emyli • 0 • updated 5 weeks ago by finswimmer • 540
1
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1
answer
180
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1
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RNA-Seq requirements for both gene expression quantification and variant calling
variant calling gene expression rna-seq written 6 weeks ago by Ozzie • 10 • updated 6 weeks ago by Devon Ryan ♦ 71k
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123
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Minimum base quality for Pindel
variant calling next-gen pindel written 7 weeks ago by jsneaththompson • 0
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122
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Disagreement in the coordinates of VCF and internal formats for Pindel
variant calling pindel written 7 weeks ago by jvel • 0
1
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1
answer
245
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1
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HaplotypeCaller filter out variants covered only in one direction
variant calling gatk haplotype caller written 8 weeks ago by stanedav • 10 • updated 8 weeks ago by pfs • 90
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1
answer
193
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1
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Retrieval of similar positions from samples in a vcf but different from reference
vcf variant calling bcftools written 10 weeks ago by bioinfo8 • 90 • updated 10 weeks ago by guillaume.rbt • 340
14
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7
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983
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7
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Forum: User Friendly VCF Filtering Tools
variant calling vcf forum filtering written 16 months ago by andrew.j.skelton73 • 3.9k • updated 11 weeks ago by steven.n.hart • 20
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2
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245
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2
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Variant calling step order question: base recalibration & mark duplicates, which is first?
variant calling ngs pipeline cancer written 11 weeks ago by alons • 230 • updated 11 weeks ago by Brian Bushnell ♦ 14k
2
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0
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182
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0
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Retain file names as sample names while making pileup
vcf variant calling bcftools samtools gene written 12 weeks ago by bioinfo8 • 90 • updated 12 weeks ago by WouterDeCoster ♦ 22k
6
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1
answer
335
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1
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snpEff inappropriate interpretation of variants?
software error variant calling alignment rna-seq written 12 weeks ago by moushengxu • 260 • updated 12 weeks ago by rbagnall • 1.1k
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3
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275
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7 follow
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Is it possible to run variant calling software in parallel, are there any Shell and Python/R code examples available?
vcf variant calling parallel written 3 months ago by bioinform • 20 • updated 3 months ago by vchris_ngs • 4.0k
6
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2
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246
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2
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how to calling variants in RNAseq data from multiple samples?
variant calling gatk vc rna-seq written 3 months ago by Lila M • 370 • updated 3 months ago by Samuel Brady • 230
4
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2
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385
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6 follow
2
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SNPs Calling Tools
variant calling alignment snp rna-seq written 7 months ago by dd.catania • 0 • updated 3 months ago by colindaven • 340
7
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1
answer
227
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6 follow
1
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Correct way of merging samples for father, mother, child trio variant calling
vcf variant calling bam written 3 months ago by eurioste • 20 • updated 3 months ago by Pierre Lindenbaum ♦ 99k
0
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1
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229
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1
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Extracting Codons from a SNP alignment
variant calling next-gen phylogenetics snp written 3 months ago by tpaisie • 60 • updated 3 months ago by rbagnall • 1.1k
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234
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0
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What makes low frequency variants callers good at what they do?
variant calling lofreq freebayes somatic mutation written 3 months ago by CY • 40
2
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1
answer
189
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1
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Pindel and GATK AD Concordance
variant calling gatk allele depth pindel written 4 months ago by jsneaththompson • 0 • updated 4 months ago by Dan Gaston ♦ 6.8k
4
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0
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284
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0
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Variants Calling on RNA Seq Samples
variant calling samtools rna-seq written 4 months ago by benjyrolls • 70
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4
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2.3k
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4
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Open Source Compliant Diploid Variant Caller comparable to GATK Haplotype Caller?
variant calling gatk written 3.0 years ago by 14134125465346445 • 3.3k • updated 5 months ago by vdauwera • 560
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2
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2
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News: Webinar on fast and accurate DNA variant calling on 26 Apr 2017
variant calling news snp gatk alignment strand ngs written 6 months ago by strandbiz • 60
3
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1
answer
1.4k
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1
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Filter/Annotate VCF with dbSNP during variant calling workflow
variant calling vcf ngs bam dbsnp written 2.3 years ago by alons • 230 • updated 5 months ago by Biostar ♦♦ 20
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200
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Freebayes is slow and maybe inaccurate when processing a single aligned read
variant calling sequencing written 5 months ago by angrypigeon • 80
0
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1
answer
257
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1
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Depth of coverage in Bam file does not match depth in VCF file
indel variant calling pindel coverage igv written 5 months ago by jsneaththompson • 0 • updated 5 months ago by tangming2005 • 2.2k
2
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1
answer
255
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1
answer
Calling SNPs with samtools: how to specify how many supporting observations are required?
variant calling samtools snps freebayes written 6 months ago by Lina F • 110 • updated 6 months ago by Brian Bushnell ♦ 14k
4
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1
answer
338
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6 follow
1
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samtools variant calling workflow
variant calling realignment samtools written 6 months ago by mirza • 80 • updated 6 months ago by Santosh Anand • 3.0k
3
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1
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266
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1
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Variant callers reporting different read depth on same alignment
variant calling gatk freebayes variant annotation written 6 months ago by Lauren • 20 • updated 6 months ago by Pierre Lindenbaum ♦ 99k
1
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2
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229
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How to split Double or Multiple Nucleotide Polymorphisms (DNP) into Single Nucleotide Polymorphisms (SNP)?
variant calling vcf snp written 6 months ago by rafa.rios.50 • 40 • updated 6 months ago by harold.smith.tarheel • 3.9k
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