Is there a convention to distinguish between heterozygous indels and homozygous indels in samtools' pileup? I have been running under the assumption that they look like I describe below, but looking at the indel frequency conditioned on the call on some simulated data there seems to be a fair number of heterozygotes that should have been called homozygous. Maybe pileup does not distinguish between het/hom in indels?
HET
HET
HOM
UNKNOWN (Multiple alleles)
HET
Code:
chr22 49513623 * */-G 352 352 45 30 * -G 18 12 0 0 0
Code:
chr22 49515653 * -G/* 121 721 49 27 -G * 20 7 0 0 0
Code:
chr22 49531477 * +G/+G 42 919 45 28 +G * 23 5 0 0 0
Code:
chr22 34169351 * +CC/+C 6 290 42 12 +CC +C 8 1 3 3 0
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