User:Lindenb/Notebook/UMR915/20101015: Difference between revisions
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==Meeting== | |||
shown how to use mediawiki. | |||
[[Category:Varscan]] | [[Category:Varscan]] | ||
[[Category:Samtools]] | [[Category:Samtools]] | ||
[[Category:Pileup]] | [[Category:Pileup]] | ||
Revision as of 02:04, 16 October 2010
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.
