cosmic.vcf.idx is not right for MuTect1
caiyanzhang
beijingMember ✭
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
Best Answer
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Geraldine_VdAuwera
Cambridge, MA admin
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.
Answers
Thank you very much
Yes, it is running ,and got the result, but the option cosmic is not usefull , does it not matter to detect somatic mutation . If use it , what can I do.
@Geraldine_VdAuwera thankyou, you mean cosmic option is important to judge the somatic .
but now , if I use the cosmic option ,there was a warnning , how can I do .