I have some .bam files from WGS their average size is 70000000 KB. I called SNV by Strelka but output .vcf files are not compatible with some downstream programs so I tried Varscan, mutect2 and muse but I noticed even with 16 cpu calling mutations never finished finally session killed. even I tried mutect2 on one chromosome by L option but again takes an ages. I am wondering how people use these tools when they never gonna finished in calling mutations
My code for mutect2
java -jar /home/local/software/GATK/3.7/source/GenomeAnalysisTK.jar -T MuTect2 -R /temp/hgig/fi1d18/hs37d5.fa -I:tumor /scratch/fi1d18/example_results/1631_WTSI-COLO_075_1pre/mapped_sample/HUMAN_1000Genomes_hs37d5_genomic_WTSI-COLO_075_1pre.dupmarked.bam -I:normal /scratch/fi1d18/example_results/1631_WTSI-COLO_075_b/mapped_sample/HUMAN_1000Genomes_hs37d5_genomic_WTSI-COLO_075_b.dupmarked.bam -L 1 -o out.vcf
/home/local/software/GATK/3.7/source/varscan somatic <(samtools mpileup --no-BAQ -f /temp/hgig/fi1d18/hs37d5.fa /scratch/fi1d18/example_results/1631_WTSI-COLO_075_b/mapped_sample/HUMAN_1000Genomes_hs37d5_genomic_WTSI-COLO_075_b.dupmarked.bamm /scratch/fi1d18/example_results/1631_WTSI-COLO_075_1pre/mapped_sample/HUMAN_1000Genomes_hs37d5_genomic_WTSI-COLO_075_1pre.dupmarked.bam) /wgs --mpileup 1 --output-vcf
I selected these options on our cluster
-l walltime=36:00:00 -l nodes=1:ppn=16
But jobs never done and killed after 36 hours
What people do on such WGS files?