no item in tumor_somatic.vcf from V0.5.2

[thirtyeggs]

trafficstars

Hello,

I ran VarSim V0.5.2 with the script that had worked well with V0.5.1, and the output tumor vcf file tumor_somatic.vcf has no variant. Could you check this?

Thanks, Yun

[johnmu]

That's strange.... I didn't change any of that part. Let me have a look at this next week. Do you mind sending me the log files of the somatic run?

[thirtyeggs]

The error message in random.cosmic.err might be helpful: VarSim 0.5.2 "-maxLen" is not a valid option java -jar randvcf2vcf.jar [options...] -max_len N : Maximum variant length [99], inclusive -min_len N : Minimum variant length [1], inclusive -novel N : Average ratio of novel variants[0.01] -num_complex N : Number of complex variants (other ones) to sample [20000] -num_del N : Number of simple deletions to sample [100000] -num_ins N : Number of simple insertions to sample [100000] -num_mnp N : Number of MNPs to sample [20000] -num_snp N : Number of SNPs to sample [3000000] -prop_het N : Average ratio of novel variants[0.6] -ref file : Reference Genome [Required] -seed N : Seed for random sampling [333] -t [MALE | FEMALE] : Gender of individual [MALE] -vcf file : Known VCF file, eg. dbSNP [Required] Outputs VCF to stdout. Randomly samples variants from VCF file.

This was not shown in the previous version.

[thirtyeggs]

I would like to ask you to add a header line to tumor_somatic.vcf. Adding the definition of "SVLEN" and "SVTYPE" would also be needed because the following warnings are shown when bcftools reads the vcf files from VarSim: [W::vcf_parse] INFO 'SVLEN' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'SVTYPE' is not defined in the header, assuming Type=String

I am writing this issue here since it looks like too tiny an issue to create another thread.

[johnmu]

Thanks for reporting! Yeah, that is a known issue. We need to add a few more fields to the header. I was at a conference this week so did get a chance to look at this yet. These issues will slowly move up my pile of todo items...