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statgen / demuxlet

Genetic multiplexing of barcoded single cell RNA-seq
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Explictly warn/fail when an indel is encountered #84

Open nh13 opened 3 years ago

nh13 commented 3 years ago

Currently, on the first base in the ref/alt alleles are stored and compared, which can lead to misleading results if the input VCF has indels. See this line: https://github.com/statgen/demuxlet/blob/537ba9478b9bc0aa9d8898520ed03ef44564c7df/cmd_cram_demuxlet.cpp#L322

nh13 commented 3 years ago

The current behavior is that any read will be counted towards the reference allele.

yimmieg commented 3 years ago

Hi Nils,

Thank you for bringing this up. Hyun may have some bandwidth to push a commit to fix this.

J

Sent from a phone. Excuse the typos.

On Jan 20, 2021, at 12:38 PM, Nils Homer notifications@github.com wrote:

 The current behavior is that any read will be counted towards the reference allele.

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nh13 commented 3 years ago

Excellent! I think the main issue is that it is comparing the first base in the allele, versus the full allele from the VCF and the bases starting at the mapped position the the read.