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bmvdgeijn / WASP

WASP: allele-specific pipeline for unbiased read mapping and molecular QTL discovery
Apache License 2.0
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Sum of reads breakdown not equal to total reads #63

Open yjqiu opened 7 years ago

yjqiu commented 7 years ago

I checked the output log file for find_instersecting_snps. But when I noticed that the sum of indels, excess overlapping SNPs, keep, remap, and excess allelic combinations is larger than the total number of reads in the bam file. Any ideas why this happen?

yjqiu commented 7 years ago

I think I kind of figured it out. For keep, remap, and excess overlapping snps, the script adds one. For indels and excess allelic combinations, the script adds two. Also, for filter_reampped_reads the script outputs the number of reads instead of read pairs. It would be better if it can be consistent.