Add chrom regex filter #11
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juhis
reviewed
Apr 20, 2021
| @@ -19,6 +19,7 @@ | |||
| "saige.test_combine.test.minmac": 5, | |||
| "saige.test_combine.test.logP": true, | |||
| "saige.test_combine.combine.logP": true, | |||
| "saige.test_combine.combine.chrom_regex": "^chr(([0-9]{1,2})|([XYM]))$", | |||
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Not relevant for current functioning but while at this I would make chr optional in case this is used for data without a chr prefix. Also would add XYMT in case there's mitochondrial as MT
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Then, how about this:
Suggested change
| "saige.test_combine.combine.chrom_regex": "^chr(([0-9]{1,2})|([XYM]))$", | |
| "saige.test_combine.combine.chrom_regex": "^(chr)?(([0-9]{1,2})|([XYM]|MT))$", |
Now chr is optional (matched 0 or 1 times) and chromosome can be 0-99, X,Y,M,MT
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Sometimes the data contains some odd contigs. Added an input to the saige_sub.wdl to filter chromosomes based on a regex (saige.test_combine.combine.chrom_regex), which by default should be
chr([0-9]{1,2})|(XYM)\sto include chr1-22, chrX, chrY, chrM.