User:Lindenb/Notebook/UMR915/20101015

20101014        Top        20101018       

Testing Varscan for our data

 for I in 1....
 do
 	for PROG in pileup2snp pileup2indel
 	do
 		echo "prog:${PROG} indi:${I}"
 		   samtools-0.1.7a/samtools pileup \
 			-f hg18.fa \
 			recal_bwa_rmdup_XXXX${I}.bam |\
 		java -jar VarScan.v2.2.jar ${PROG} | gzip > varscan_${PROG}_${I}.tsv.gz
 	done
 done

Meeting

shown how to use mediawiki.