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statgen / demuxlet

Genetic multiplexing of barcoded single cell RNA-seq
Apache License 2.0
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GL vs PL for genotype likelihood #12

Open acwarren opened 6 years ago

acwarren commented 6 years ago

Freebayes outputs VCFs with genotype likelihoods of format GL (which are not phred scaled) instead of PL, but I found that demuxlet failed to produce reasonable results using those as the field input. Do you have a script that converts GL to PL or what is the expected input/what platform was used to create the input VCF files? Thanks

yimmieg commented 6 years ago

can you elaborate a little bit more on this? others have called variants with GATK and that seems to work fine.