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9
votes
2
answers
214
views
5 follow
2
answers
DNA sequence of genes from vcf file
vcf variant calling bcftools gene ensembl written 18 days ago by bioinfo8 • 80 • updated 4 days ago by Whoknows • 580
2
votes
1
answer
112
views
1
answer
Retrieval of similar positions from samples in a vcf but different from reference
vcf variant calling bcftools written 5 days ago by bioinfo8 • 80 • updated 5 days ago by guillaume.rbt • 290
14
votes
7
answers
840
views
7
answers
Forum: User Friendly VCF Filtering Tools
variant calling vcf forum filtering written 14 months ago by andrew.j.skelton73 • 3.6k • updated 14 days ago by steven.n.hart • 20
2
votes
2
answers
186
views
2
answers
Variant calling step order question: base recalibration & mark duplicates, which is first?
variant calling ngs pipeline cancer written 15 days ago by alons • 220 • updated 15 days ago by Brian Bushnell ♦ 13k
2
votes
0
answers
130
views
0
answers
Retain file names as sample names while making pileup
vcf variant calling bcftools samtools gene written 19 days ago by bioinfo8 • 80 • updated 19 days ago by WouterDeCoster ♦ 20k
6
votes
1
answer
223
views
1
answer
snpEff inappropriate interpretation of variants?
software error variant calling alignment rna-seq written 23 days ago by moushengxu • 260 • updated 22 days ago by rbagnall • 1.1k
9
votes
3
answers
222
views
7 follow
3
answers
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 25 days ago by bioinform • 20 • updated 25 days ago by vchris_ngs • 3.7k
6
votes
2
answers
189
views
2
answers
how to calling variants in RNAseq data from multiple samples?
variant calling gatk vc rna-seq written 5 weeks ago by Lila M • 320 • updated 4 weeks ago by Samuel Brady • 230
4
votes
2
answers
330
views
6 follow
2
answers
SNPs Calling Tools
variant calling alignment snp rna-seq written 5 months ago by dd.catania • 0 • updated 5 weeks ago by colindaven • 260
7
votes
1
answer
163
views
6 follow
1
answer
Correct way of merging samples for father, mother, child trio variant calling
vcf variant calling bam written 6 weeks ago by eurioste • 20 • updated 6 weeks ago by Pierre Lindenbaum ♦ 96k
0
votes
1
answer
183
views
1
answer
Extracting Codons from a SNP alignment
variant calling next-gen phylogenetics snp written 7 weeks ago by tpaisie • 60 • updated 6 weeks ago by rbagnall • 1.1k
0
votes
0
answers
170
views
0
answers
What makes low frequency variants callers good at what they do?
variant calling lofreq freebayes somatic mutation written 7 weeks ago by CY • 30
2
votes
1
answer
129
views
1
answer
Pindel and GATK AD Concordance
variant calling gatk allele depth pindel written 10 weeks ago by jsneaththompson • 0 • updated 10 weeks ago by Dan Gaston ♦ 6.8k
4
votes
0
answers
208
views
0
answers
Variants Calling on RNA Seq Samples
variant calling samtools rna-seq written 11 weeks ago by benjyrolls • 70
21
votes
4
answers
2.3k
views
4
answers
Open Source Compliant Diploid Variant Caller comparable to GATK Haplotype Caller?
variant calling gatk written 2.9 years ago by 14134125465346445 • 3.3k • updated 12 weeks ago by vdauwera • 560
0
votes
2
answers
215
views
2
answers
News: Webinar on fast and accurate DNA variant calling on 26 Apr 2017
variant calling news snp gatk alignment strand ngs written 4 months ago by strandbiz • 60
3
votes
1
answer
1.3k
views
1
answer
Filter/Annotate VCF with dbSNP during variant calling workflow
variant calling vcf ngs bam dbsnp written 2.1 years ago by alons • 220 • updated 3 months ago by Biostar ♦♦ 20
0
votes
0
answers
153
views
0
answers
Freebayes is slow and maybe inaccurate when processing a single aligned read
variant calling sequencing written 3 months ago by angrypigeon • 80
0
votes
1
answer
181
views
1
answer
Depth of coverage in Bam file does not match depth in VCF file
indel variant calling pindel coverage igv written 3 months ago by jsneaththompson • 0 • updated 3 months ago by tangming2005 • 2.1k
2
votes
1
answer
199
views
1
answer
Calling SNPs with samtools: how to specify how many supporting observations are required?
variant calling samtools snps freebayes written 3 months ago by Lina F • 100 • updated 3 months ago by Brian Bushnell ♦ 13k
3
votes
1
answer
263
views
1
answer
samtools variant calling workflow
variant calling realignment samtools written 4 months ago by mirza • 70 • updated 4 months ago by Santosh Anand • 2.8k
3
votes
1
answer
197
views
1
answer
Variant callers reporting different read depth on same alignment
variant calling gatk freebayes variant annotation written 4 months ago by Lauren M. • 10 • updated 4 months ago by Pierre Lindenbaum ♦ 96k
1
vote
2
answers
181
views
2
answers
How to split Double or Multiple Nucleotide Polymorphisms (DNP) into Single Nucleotide Polymorphisms (SNP)?
variant calling vcf snp written 4 months ago by rafa.rios.50 • 40 • updated 4 months ago by harold.smith.tarheel • 3.7k
2
votes
1
answer
254
views
1
answer
Best pratices for variant calling on deep sequencing TruSeq Custom Amplicon data
variant calling amplicon sequencing written 4 months ago by adp7 • 10 • updated 4 months ago by igor • 4.4k
3
votes
0
answers
298
views
5 follow
0
answers
News: Workshop: GATK Best Practices for Variant Discovery, Edinburgh, 17-19 July 2017
variant calling gatk news workshop written 4 months ago by Bert Overduin • 3.5k
0
votes
0
answers
202
views
0
answers
Merging VCFs: Illumina/GATK and LoFreq
variant calling vcf miseq written 4 months ago by ari.nazarian • 0
3
votes
2
answers
532
views
8 follow
2
answers
extract SNP, variants
indel variant calling snp rna-seq mapping written 4 months ago by divya • 10 • updated 4 months ago by AB • 60
1
vote
0
answers
262
views
0
answers
How come female has variants in chrY and How come male variants in chrX are represented as two alleles?
variant calling snp rna-seq variants written 4 months ago by genomicsngs2017 • 0
2
votes
1
answer
181
views
1
answer
Outputting DP4 flag in GATK
variant calling gatk sequencing written 4 months ago by Jautis • 240 • updated 4 months ago by Santosh Anand • 2.8k
0
votes
0
answers
158
views
0
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Variant calling on sample from both Illumina and Proton technology
variant calling proton floworder written 4 months ago by haro • 150
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