suppress indel/snp calling to reduce running time

xulab-nwafu · Jan 3, 2018 · 896deec · 896deec
1 parent ee1398c
commit 896deec
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diff --git a/LICENSE b/LICENSE
@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2016-2017 Xu Lab, Northwest A&F University
+Copyright (c) 2016-2018 Xu Lab, Northwest A&F University
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/README.md b/README.md
@@ -5,7 +5,7 @@ The `hits` is an integrated pipeline for DNA resequencing and RNAseq analyses in
 HIgh-Throughput Sequencing (hits) pipeline
 ------------------------------------------
 ```
-hits 0.4.2
+hits 0.4.3
 
 Usage:
 
@@ -94,7 +94,7 @@ Qinhu Wang (wangqinhu@nwafu.edu.cn)
 
 Copyright
 ---------
-2016-2017 (c) Xu Lab, Northwest A&F University
+2016-2018 (c) Xu Lab, Northwest A&F University
 
 License
 -------

diff --git a/hits b/hits
@@ -10,7 +10,7 @@ use warnings;
 use Getopt::Std;
 
 my $appname = 'hits';
-my $version = '0.4.2';
+my $version = '0.4.3';
 my %options = ();
 
 init();
@@ -70,10 +70,6 @@ sub dnaseq {
 		print STDERR "Calling variants ...\n";
 		my $callvar_cmd = "samtools mpileup -uf $options{'g'} $dir/bam/$fq.bam | bcftools call --ploidy 1 -cv -O v - > $dir/vcf/$fq.vcf";
 		system($callvar_cmd);
-		my $callsnp_cmd = "samtools mpileup -uf $options{'g'} $dir/bam/$fq.bam | bcftools call --ploidy 1 -cv -V indels -O v - > $dir/vcf/$fq.snps.vcf";
-		system($callsnp_cmd);
-		my $callindel_cmd = "samtools mpileup -uf $options{'g'} $dir/bam/$fq.bam | bcftools call --ploidy 1 -cv -V snps -O v - > $dir/vcf/$fq.indels.vcf";
-		system($callindel_cmd);
 	}
 
 	print STDERR "Done\n\n";