From 115a593f66964894c8fe60287493914dcea63f56 Mon Sep 17 00:00:00 2001 From: jlac Date: Wed, 16 Oct 2019 09:24:13 -0400 Subject: [PATCH] fixed gzipped VCF issue with germline calling --- Rules/admixture_germline.rl | 2 +- Rules/make.germline.network.rl | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/Rules/admixture_germline.rl b/Rules/admixture_germline.rl index 48a623d..91ed0aa 100755 --- a/Rules/admixture_germline.rl +++ b/Rules/admixture_germline.rl @@ -1,5 +1,5 @@ rule admixture_germline: - input: "exome.strictFilter.vcf.gz" + input: "exome.strictFilter.vcf" output: vcf=temp("admixture_out/samples_noINDEL_nomissing.recode.vcf"), mergedvcf=temp("admixture_out/samples_and_knowns.vcf"), ped=temp("admixture_out/samples_and_knowns_filtered.ped"), diff --git a/Rules/make.germline.network.rl b/Rules/make.germline.network.rl index 57e99a8..727878d 100755 --- a/Rules/make.germline.network.rl +++ b/Rules/make.germline.network.rl @@ -1,5 +1,5 @@ rule make_germline_network: - input: "exome.strictFilter.vcf.gz" + input: "exome.strictFilter.vcf" output: network="sample_network_mqc.png", params: rname="make.germline.network" shell: """