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10 votes
Accepted

Single-sample vs. joint genotyping

Say you are sequencing to 2X coverage. Suppose at a site, sample S has one reference base and one alternate base. It is hard to tell if this is a sequencing error or a heterozygote. Now suppose you ...
  • 6,053
8 votes
Accepted

Is spark widely used in bioinformatics?

The only bioinformatics tool other than GATK4 that I am aware of that uses spark is Hail (a Spark based replacement for Plink). Hail is also supported by researchers at the Broad. Most places I have ...
  • 2,146
8 votes
Accepted

Converting VCF file to PLINK bed/bim/fam files

Given that Plink reads in VCF files natively, and Plink is your desired output format, I expect that plink --vcf <file> would be the best option. As mentioned ...
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6 votes

Is spark widely used in bioinformatics?

I think others have provided fine answers to your question already. I just thought it might be relevant to mention about a tool that allows using Spark to distribute computations that re-use existing ...
6 votes

Is spark widely used in bioinformatics?

ADAM and avocado are Spark-based alignment and variant calling tools under active development by a collaboration (http://bdgenomics.org) that also includes the Broad, but I do not believe they have ...
6 votes

Variant calling without matched normal sample

If you just want to filter out calls present in dbSNP then use: ...
  • 19.3k
5 votes
Accepted

Marking optical or PCR duplicates with picard vs. samtools flagstat

There are duplicates, in this line: 1636809 + 0 duplicates, gives 1636809/26595942 = 0.06154356 According to samtools documentation for flagstat: Provides counts for each of 13 categories based ...
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5 votes
Accepted

Where can I get the population allele frequency vcf file?

On the GATK forum they've recommended the population stratified VCF file for this purpose.
  • 19.3k
5 votes
Accepted

snakemake multiple parameters for multiple input and single output in snakemake. ConbineGVCFs gatk problem

Found out the problem. Turns out I can write a lambda function as follows params: extra=lambda wildcards, input: ' -V '.join(input.all_gvcf_list) and add '-...
4 votes

Merge 2 VCFs from different variant callers

The merge utility from SURVIVOR seems to be what you are looking for. I did not try it yet, but it seems to be especially designed to handle SV. The simplest thing to do would probably to first merge ...
  • 595
4 votes

No variant found using GATK 4.0 HaplotypeCaller

As well as the issues @sjcockell mentions, you have another potential problem you've got a hexaploid organism, by default the HaplotypeCaller (HC) is hardwired to a ploidy of 2, you need to set this ...
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4 votes
Accepted

How to convert a BAM file into a VCF file

To go from .bam to .vcf, it is fairly easy using bcftools call: ...
  • 1,288
3 votes
Accepted

Subset a multisample VCF file

Based on the way you've called the command (using -xl-sn), I assume you are using GATK 4 and not GATK 3. If this is the case, the documentation for the ...
  • 350
3 votes
Accepted

No variant found using GATK 4.0 HaplotypeCaller

There are steps of the 'best practices' workflow missing, which I think is leading to the majority of reads being filtered by the haplotype caller, notice these lines in the output: ...
  • 861
3 votes
Accepted

Increase number of threads for GATK 4.0 HaplotypeCaller

I am assuming you are using the non-SPARK version of the method. To specify the number of threads you wish to use with HaplotypeCaller, include ...
  • 1,129
3 votes

GATK CombineVariants complains the contig order in the VCF files

Answered in the GATK forum Try regenerating the index files for your VCFs. Picard SortVcf doesn't do it for you iirc, so when GATK looks at the index files (before opening the VCFs themselves) it ...
3 votes

Targeted NGS, up to 99% of reads have been marked as duplicates

If you're doing target capture, especially of a small region, it is entirely possible that there are only five unique reads. Target capture is molecularly finicky and sometimes the entire region is ...
  • 3,091
3 votes

Converting VCF file to PLINK bed/bim/fam files

Additional tidbit I learned in the last year that I wanted to share with anyone else that's working on this. Plink creates an extremely generic fam file for you, but if you are updating this fam file ...
  • 465
3 votes

Convert VCF file to mpileup.txt

Going VCF to mpileup is not really something one does or can do. The mpileup should be generated from a BAM or SAM file or something else that has raw, unfiltered read alignments in it. The VCF just ...
2 votes

Single-sample vs. joint genotyping

The benefit to additional samples is seen in your point 1. The likelihood of making a variant call is a function of (1) the depth of coverage supporting a given variant (ignoring mapping/base quality ...
  • 19.3k
2 votes
Accepted

GATK documentation for required depth to reliably call heterozygous mutation in diploid organism?

UPDATE: As an update, Sarah Walker (co-author on the poster) responded to my question on the GATK forum. She clarified with the following statement: We believe ...
  • 1,264
2 votes
Accepted

Human Genome Alignment and Variant Calling Benchmarks

NA12878 My recommendation: download raw reads from Illumina BaseSpace and do alignment yourself. Aligning ~40X worth of human reads takes overnight with ~16 CPU cores. You can acquire Platinum Genome ...
  • 6,053
2 votes
Accepted

GATK CombineVariants complains the contig order in the VCF files

GATK cannot combine VCF files generated by Sniffles, the variant caller that I used to call structural variants (answer from the GATK team).
2 votes
Accepted

No MQ tags in VCF files

As @ATpoint explains in his comment, the mapping quality (MQ) applies to read mappings and, hence, is contained in BAM files, but not VCFs. The ...
  • 353
2 votes

How to generate the json files for Cromwell workflow execution?

Unfortunately generating inputs for Cromwell is not something that is handled by Cromwell itself or by GATK, and generally needs to be scripted to fit your custom needs. Despite this being a bit ...
2 votes

Marking optical or PCR duplicates with picard vs. samtools flagstat

@StupidWolf's answer is correct -- that first number in the flagstat output is what you want to look at to see the number of reads marked as duplicates. I wanted to add that the number given in the ...
2 votes

Low pass sequencing has been reported to detect common variants. How low can one go and get reliable data? Is 2X pass sequencing analysis possible?

This is a good idea - low pass sequencing has shown to be better than genotype arrays for things such as GWAS or QTL mapping. The primary way of processing low-pass sequencing data is to use ...
  • 1,288
2 votes

Best practice for running GATK VQSR on X chromosome

You are correct that differences in ploidy between autosomes (always ploidy=2) and X chromosome mean that the same VQSR model cannot be applied to both cases equally. However, this is the case only ...
  • 527
2 votes

Error in running Mutect2

Your input file pon.vcf.gz should be a gzip file, but from your file command it looks like it is an HTML file instead. Perhaps ...
  • 2,146

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