Question: Can anyone tell me why BCFTools Call would call a homozygous variant at this position with 1/2 alt variant reads?
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gravatar for fwuffy
2.4 years ago by
fwuffy100
Michigan, USA
fwuffy100 wrote:

Here's a variant SNP with raw depth of 2, and DP4 field shows 1 alt-forward read. Can someone help me understand why this is called homozygous 1/1 at this position intead of hetero 0/1? (I am filtering out calls with DP < 5 after this, but it still raises questions)

Thanks!

samtools mpileup -v -u -B -t DP -f ref.fa mapped-sorted-mkdup.bam | bcftools call -c -v - > variants.vcf

chr19 3136246 . A G 14.1809 . DP=2;SGB=-0.379885;MQ0F=0;AF1=1;AC1=2;DP4=0,0,1,0;MQ=60;FQ=-29.9903;ANN=G|5_prime_UTR_variant|MODIFIER|GNA15|GNA15|transcript|NM_002068.3|protein_coding|1/7|c.-205A>G|||||205|,G|downstream_gene_variant|MODIFIER|LOC390876|LOC390876|transcript|TRANSCRIPT_LOC390876|pseudogene||n.*4809A>G|||||4809| GT:PL:DP 1/1:44,3,0:1

Edit: I may have answered my own question, in that there should be a value in the ref fwd/ref reverse DP4 positions to make a heterozygous call, which are probably missing due to low quality, but I'll leave this up in case people have something to add...

like "Sum can be smaller than DP because low-quality bases are not counted."

variants bcftools vcf • 1.2k views
ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by fwuffy100

Yes, you have answered your own question. DP is the total reads at the position, whilst DP4 relates to 'high quality' reads.

Still, it is suspect to call homozygous from just a single read and, just to be sure, do not in any way base any clinical decision on this variant ;)

ADD REPLYlink written 2.4 years ago by Kevin Blighe63k
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