Mercurial > repos > biomonika > linkyx
diff LINKYX_mpileup_wrapper.sh @ 2:0d8315be76b7
Uploaded
| author | biomonika |
|---|---|
| date | Tue, 17 Feb 2015 21:59:51 -0500 |
| parents | 05c27700e5ca |
| children |
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--- a/LINKYX_mpileup_wrapper.sh Sun Sep 07 23:12:26 2014 -0400 +++ b/LINKYX_mpileup_wrapper.sh Tue Feb 17 21:59:51 2015 -0500 @@ -5,8 +5,4 @@ sorted_bam=${bam_file}_sorted -#LINKYX_PATH set during toolshed installation - samtools mpileup -uf $reference $bam_file 2>log.txt | bcftools view -p 0.85 -cgv - 2>log.txt >$results - -#samtools mpileup -uf $reference $2 2>log.txt | bcftools view -p 0.85 -cgv - 2>>log.txt| vcfutils.pl varFilter >$results 2>>log.txt \ No newline at end of file