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Call somatic short variants with mutect - BAM file contigs not matching the reference
Dear GATK Staff,
I read a lot about this problem however it still occurs. I think I did all that I can withouts succes. Here is my run-function based on your tutorial about calling somatic variants:
gatk --java-options "-Xmx2g" Mutect2 \ -R ucsc.hg19.fasta \ -I 1_Tumor_sorted_markduplicates_RG.bam \ -I 1_Blood_markduplicates_RG.bam \ -tumor 1_tumor \ -normal 1_normal \ -pon 1_2_3_threesamplepon_chr.vcf.gz \ --germline-resource af-only-gnomad.raw.sites.hg19.vcf.gz \ --af-of-alleles-not-in-resource 0.0000025 \ --disable-read-filter MateOnSameContigOrNoMappedMateReadFilter \ -O P129_somatic_m2.vcf.gz \ -bamout P129_tumor_normal_m2.bam
All reference files I found here:
Unfortunately it's still a problem with chromosome names:
reads contigs = [chr1, chr2, chr3, chr4, chr5....] reads features = [1,2,3....]
I checked everything, the lengths and names of chromosomes of my .bam files are exactly the same as in the reference.
samtools view -H 1_Tumor_sorted_markduplicates_RG.bam |grep '^@SQ'>chromosomes.txt
same as in here:
samtools idxstats 1_Tumor_sorted_markduplicates_RG.bam | head -n 3
Each starts with 'chr'.
In the reference, also record in fasta starts with 'chr'.
In case of 1_2_3_threesamplepon_chr.vcf.gz I also checked it, each row after header starts with 'chr'.
af-only-gnomad.raw.sites.hg19.vcf.gz - also each row after header starts with 'chr'...
Everything is fine, but it doesn't work, there's always a problem, always an error, on each step of the analysis - based on your tutorial...
I'm fighting with this since monday during whole days... Please, could you help me?