VAF/EAF scores #8
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…r PASS and extra FORMAT tags for VAF and EAF values
…sitions, both varScoreVAF and varScoreEAF fields
…F quality scores in the output
…_position() function; return at line 405 needs fixing later
…sitions if qual_scores = true, otherwise passes and empty list
…n; also to the embebbed function process_allele(); In case of a variant, yield now includes the list of quality scores in the returned dictionary; added also qual_scores argument to the embebbed process_full/split_positions calls that handle the last line
…s_allele(); if qual_scores is True, both VAF and EAF scores will be stored and computed as mean if more than one is present for a given locus. These will be returned as a list
…es if present; extra fixings mighr be needed
… are passed to the yield; now it is a string not a list. // Also fix in the process_allele() function
…header accordingly
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Complete Genomics varfiles have two columns with the quantitative scores varScoreVAF and varScoreEAF, which are given whenever a position has an alternate allele (absent in full ref calls or no-calls).
These proposed changes simply add to the base code the optional ability to output and keep these scores into the gVCF/VCF if the user wants it.
Your base code is beautiful and elegant. I have learned many things while working with it.
Thanks for sharing