User:Lindenb/Notebook/UMR915/20101118: Difference between revisions
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samtools-0.1.10/samtools index jeter.bam | samtools-0.1.10/samtools index jeter.bam | ||
java -jar GenomeAnalysisTK.jar -T UnifiedGenotyper -R /GENOTYPAGE/data/pubdb/ucsc/hg18/chromosomes/hg18.fa -I jeter.bam -o snps.raw.vcf -D /GENOTYPAGE/data/pubdb/broad.mit.edu/gsa/resources/dbsnp_129_hg18.rod -stand_call_conf 50.0 -stand_emit_conf 10.0 -dcov 50 > jeter.vcf | java -jar GenomeAnalysisTK.jar -T UnifiedGenotyper -R /GENOTYPAGE/data/pubdb/ucsc/hg18/chromosomes/hg18.fa -I jeter.bam -o snps.raw.vcf -D /GENOTYPAGE/data/pubdb/broad.mit.edu/gsa/resources/dbsnp_129_hg18.rod -stand_call_conf 50.0 -stand_emit_conf 10.0 -dcov 50 > jeter.vcf | ||
hum.. it doesn't count the INDELS | |||
Revision as of 04:17, 18 November 2010
Integragen
creating custom reports for Cedric
Samtools
updating samtools-0.1.10.tar.bz2 (prev version was 1.7 )
Belgium
MosaikSort -in align1.mka -out align1.sorted.mka MosaikText -in align1.sorted.mka -bam jeter.bam samtools-0.1.10/samtools index jeter.bam java -jar GenomeAnalysisTK.jar -T UnifiedGenotyper -R /GENOTYPAGE/data/pubdb/ucsc/hg18/chromosomes/hg18.fa -I jeter.bam -o snps.raw.vcf -D /GENOTYPAGE/data/pubdb/broad.mit.edu/gsa/resources/dbsnp_129_hg18.rod -stand_call_conf 50.0 -stand_emit_conf 10.0 -dcov 50 > jeter.vcf
hum.. it doesn't count the INDELS
