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Hi all,
I have used SAMtools pileup in order to identify indels. According to this page, there should be 13 columns.
My output has 15 columns, and most of the lines make sense, e.g.:
I assumed that the sum of columns 11, 12, and 13 would equal column 8. This holds for most of the indels, but I noticed it doesn't hold for all.
There are certain regions with very high read depths and which do not satisfy (c11+c12+c13)==c8. Example:
When I view this region in IGV (screenshot), it looks poorly mapped but definitely not read depths of ~10k.
Any ideas on why this might be?
I have used SAMtools pileup in order to identify indels. According to this page, there should be 13 columns.
My output has 15 columns, and most of the lines make sense, e.g.:
Code:
chr1 107591963 * */-TC 69 69 59 91 * -TC 86 5 0 0 0
There are certain regions with very high read depths and which do not satisfy (c11+c12+c13)==c8. Example:
Code:
chr2 98507236 * */* 2652 0 28 7999 * -T 1019 5 0 0 0 chr2 98507238 * */* 2619 0 28 8001 * -G 1022 1 1 1 964 chr2 98507239 * */* 2800 0 28 8000 * -A 1017 6 1 0 0 chr2 98507245 * */* 2947 0 28 7990 * -G 1022 2 0 0 0 chr2 98507247 * */* 2990 0 29 7998 * -C 1021 3 0 0 0 chr2 98507249 * */* 3016 0 29 7992 * -A 1023 1 0 0 0
Any ideas on why this might be?
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