Question: SAM/BCF tools output alternate counts
gravatar for jodyphelan
3.5 years ago by
jodyphelan0 wrote:

I have a single sample BAM file and sometimes there may be more than one allele at a single position (either true or sequencing error) I am trying to output the read counts supporting each alternate allele at site.

samtools mpileup -ugf <ref.fa> <bamfile> | bcftools call --ploidy 1 -AmO v (htslib version 1.4)

For example it outputs like this: Chromosome 3913737 . G A 24.8295 . DP=91;VDB=0.322194;SGB=-0.693143;RPB=0.982146;MQB=1;MQSB=1;BQB=0.99872;MQ0F=0;AC=0;AN=1;DP4=21,8,26,12;MQ=60 GT:PL 0:255,255

From the header it looks like the AC info flag should output this information (##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes for each ALT allele, in the same order as listed">) However as you can see the DP4 looks like there are many alternare allele reads present but AC=0.

Does anyone have any suggestions?

ADD COMMENTlink modified 3.5 years ago by Pierre Lindenbaum131k • written 3.5 years ago by jodyphelan0
gravatar for Pierre Lindenbaum
3.5 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum131k wrote:

The genotype is REF type (allele=0, GT=0)

 GT:PL 0:255,25

and the number of ALT tlernative Allele count is 0

The sample in the first column is not mutated at this position.

ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by Pierre Lindenbaum131k
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