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somatic vcf is empty #275

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Tina610 opened this issue Oct 8, 2023 · 0 comments
Open

somatic vcf is empty #275

Tina610 opened this issue Oct 8, 2023 · 0 comments

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@Tina610
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Tina610 commented Oct 8, 2023

hi,I'm using varsim_somatic(docker:rssbred/varsim),I got cosmic_somatic.vcf has no variant. My command is :

/opt/varsim/varsim_somatic.py --reference ref_out/my_ref.fasta --id cosmic --som_num_snp 20 --som_num_ins 20 --som_num_del 20 --som_num_mnp 20 --som_num_complex 20 --cosmic_vcf CosmicCodingMuts_COSMICv96.vcf.gz --normal_vcf test.truth.vcf --nlanes 1 --total_coverage 800 --simulator art --profile_1 HiSeqXtruSeqL150R1.txt --profile_2 HiSeqXtruSeqL150R2.txt --simulator_executable art_illumina --out_dir varsim_test5 --log_dir log --work_dir workdir --read_length 150 --sv_insert_seq insert_seq.txt --java_max_mem 50g --somatic_vcfs somatic.vcf

Can you help me to troubleshoot this issue?
ps:my reference file region(by generate_small_test_ref.py) covers the somatic_vcf region

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