Commit 6e3205d1 authored by van den Berg's avatar van den Berg
Browse files

Add constant GVCF bands with 20GQ increments

By default, GATK will group regions into 100 GQ bins,
with each bin containing only regions with the exact
specified GQ. This leads to large files wich are slow
to parse, while such a high resolution of GQ scores is
most likely not needed.
parent 74dd7e6c
Pipeline #3521 failed with stages
in 1 minute and 55 seconds
......@@ -359,7 +359,9 @@ rule gvcf_scatter:
"{input.bam} -R {input.ref} -D {input.dbsnp} "
"-L '{input.region}' -o '{output.gvcf}' "
"-variant_index_type LINEAR -variant_index_parameter 128000 "
"-BQSR {input.bqsr}"
"-BQSR {input.bqsr} "
"--GVCFGQBands 20 --GVCFGQBands 40 --GVCFGQBands 60 "
"--GVCFGQBands 80 --GVCFGQBands 100 "
def aggregate_gvcf(wildcards):
checkpoint_output = checkpoints.scatterregions.get(**wildcards).output[0]
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