'Number of alignments skipped due to not being useful'

10XGenomics / vartrix

Single-Cell Genotyping Tool

MIT License

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'Number of alignments skipped due to not being useful' #32

Closed Puriney closed 4 years ago

Puriney commented 4 years ago

Hello vartrix team, I was wondering what does the 'Number of alignments skipped due to not being useful' means, as the majority of my alignments fall into this category. Thanks.

pmarks commented 4 years ago

Many alignments in the BAM file produced by STAR have long 'refskip' cigar entries which cause a large gap in the alignment where no read bases are aligned to the reference. STAR creates lots of these records. If one of these gaps covers the SNP location, then the read is 'skipped due to not being useful', because it didn't actually contain the variant position.