Question: Why call variant generate homozygous site with genotype 0/0, why it be reported even if it same with reference genome?
1
gravatar for Nich
9 weeks ago by
Nich10
Nich10 wrote:

Hi, guys I use gatk to call variant and get a vcf file. When I look into it, I find some homozygous site with genotype 0/0.

chr2    231861039       .       CCT     .       793     .       AN=2;DP=275;MQ=60.00    GT:AD:DP        0/0:275:275

I think this variant means it same with reference genome. So I don't know why it still been reported by SNP caller software?

snp • 173 views
ADD COMMENTlink modified 9 weeks ago by d-cameron2.0k • written 9 weeks ago by Nich10

what was the command line / version ?

ADD REPLYlink written 9 weeks ago by Pierre Lindenbaum120k

gatk gatk-4.1.0.0 HaplotypeCaller

/software/gatk4.0/gatk-4.1.0.0/gatk --java-options    '-Xmx20g'  HaplotypeCaller  -L  region.bed -R  ucsc.hg19.fasta -I ccr.bam  -O ccr.vcf     >ccr.std 2>&1

nothing special

ADD REPLYlink written 9 weeks ago by Nich10

Is this multiple sample variant calling? If so, then perhaps other samples have 0/1 and 1/1 genotypes if this is a biallelic SNP.

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by jean.elbers1.1k

I just use gatk HaplotypeCaller call one sample

ADD REPLYlink written 9 weeks ago by Nich10

Hmmm...well, after looking at your example output, it even shows there is no ALT allele. You could get rid of rows with like that with awk '$5!="."' OFS='\t' input-vcf-file > new-vcf-file-without-false-variants or something like that.

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by jean.elbers1.1k
0
gravatar for d-cameron
9 weeks ago by
d-cameron2.0k
Australia
d-cameron2.0k wrote:

Reporting homozygous reference is important as it distinguishes that position from a no call position.

To answer the question: do samples A and B have the same alleles at position X, you need to know what the alleles are in both samples. If your SNV caller is unable to call position X in one of the samples (e.g. insufficient enough coverage, read mapqs too low, ...), then the answer to that question is "I don't know".This is not the same as "hom ref in both" and "ref in one, non-ref in other" and these cases need to be treated differently.

ADD COMMENTlink written 9 weeks ago by d-cameron2.0k
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