cosmic.vcf.idx is not right for MuTect1

caiyanzhang · December 2016

I want to call somatic mutation by mutect1, but I can't find cosmic.vcf in ftp ,and I want to use new version.So
step1:download new version file cosmic
get /cosmic/grch37/cosmic/v79/VCF/CosmicCodingMuts.vcf.gz
get /cosmic/grch37/cosmic/v79/VCF/CosmicNonCodingVariants.vcf.gz

step2: add the followed contig in vcf head

contig=<ID=chrM,length=16571,assembly=hg19>

contig=<ID=chr1,length=249250621,assembly=hg19>

contig=<ID=chr2,length=243199373,assembly=hg19>

contig=<ID=chr3,length=198022430,assembly=hg19>

contig=<ID=chr4,length=191154276,assembly=hg19>

contig=<ID=chr5,length=180915260,assembly=hg19>

contig=<ID=chr6,length=171115067,assembly=hg19>

contig=<ID=chr7,length=159138663,assembly=hg19>

contig=<ID=chr8,length=146364022,assembly=hg19>

contig=<ID=chr9,length=141213431,assembly=hg19>

contig=<ID=chr10,length=135534747,assembly=hg19>

contig=<ID=chr11,length=135006516,assembly=hg19>

contig=<ID=chr12,length=133851895,assembly=hg19>

contig=<ID=chr13,length=115169878,assembly=hg19>

contig=<ID=chr14,length=107349540,assembly=hg19>

contig=<ID=chr15,length=102531392,assembly=hg19>

contig=<ID=chr16,length=90354753,assembly=hg19>

contig=<ID=chr17,length=81195210,assembly=hg19>

contig=<ID=chr18,length=78077248,assembly=hg19>

contig=<ID=chr19,length=59128983,assembly=hg19>

contig=<ID=chr20,length=63025520,assembly=hg19>

contig=<ID=chr21,length=48129895,assembly=hg19>

contig=<ID=chr22,length=51304566,assembly=hg19>

contig=<ID=chrX,length=155270560,assembly=hg19>

contig=<ID=chrY,length=59373566,assembly=hg19>

step3: sort the vcf body chr
commond: cat CosmicCodingMuts.body CosmicNonCodingVariants.body | perl -ne '{chomp;@a=split/\t/,$_;if($a[0] eq "MT"){$a[0]="M"}$hash{$a[0]}{$a[1]}=join "\t",@a;}END{foreach $s (sort {$a<=>$b} keys %{$hash{M}}){print "chr$hash{M}{$s}\n"}for ($c=1;$c<=22;$c++){foreach $s (sort {$a<=>$b} keys %{$hash{$c}}){print "chr$hash{$c}{$s}\n"}}foreach $s (sort {$a<=>$b} keys %{$hash{X}}){print "chr$hash{X}{$s}\n"}foreach $s (sort {$a<=>$b} keys %{$hash{Y}}){print "chr$hash{Y}{$s}\n"} }' > All.body

step4:cat head and body
commond: cat vcf.head.m All.body >cosmic.vcf

step5:make cosmic.vcf.idx
commond: igvtools index cosmic.vcf

step6:run mutect1
java -jar /lustre/work/shufan/soft/MuTect/mutect-1.1.7.jar -T MuTect -R /lustre/database/caiyanzhang/reference/human/hg19/ucsc/ucsc.hg19.fasta -I:tumor /lustre/work/shufan/test/Human/Analysis/Picard_MarkDuplicates/100298/10298.dedup.bam -I:normal /lustre/work/shufan/test/Human/Analysis/Picard_MarkDuplicates/100298-3/dedup.bam -dbsnp /lustre/database/caiyanzhang/reference/human/hg19/annotation_vcf/dbsnp_138.hg19.vcf -cosmic /lustre/work/shufan/Database/Cosmic/grch37/v79/cosmic.vcf -L mutect.bed -o somatic.call_stats.txt -cov somatic.coverage.wig.txt

I get the information
WARN 16:28:34,093 FSLockWithShared$LockAcquisitionTask - WARNING: Unable to lock file /lustre/work/shufan/Database/Cosmic/grch37/v79/cosmic.vcf.idx because an IOException occurred with message: Function not implemented.
INFO 16:28:34,095 RMDTrackBuilder - Could not acquire a shared lock on index file /lustre/work/shufan/Database/Cosmic/grch37/v79/cosmic.vcf.idx, falling back to using an in-memory index for this GATK run.

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cosmic is not work , I thought cosmic.vcf.idx , but I don't know how to creat it right , please help me

Geraldine_VdAuwera · December 2016

I think there is nothing wrong with your cosmic and index file. The program is complaining about a function called file locking that doesn't work on your system. That is okay, it is not a failure, just a warning. This may just consume more memory than expected. The run should still continue.

Geraldine_VdAuwera · December 2016