extracting heterozygotes in rules.extract_hets

aryarm / as_analysis

A complete Snakemake pipeline for detecting allele specific expression in RNA-seq

MIT License

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Closed aryarm closed 6 years ago

aryarm commented 6 years ago

Currently, the pipeline uses grep '0|1' to extract heterozygotes from the counts. However, grep '1|0' should also be allowed.

[x] revise the grep command to allow both 0|1 and 1|0
[x] revise the grep command to be more specific (ie also match whitespace around the genotype fields)