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cortes-ciriano-lab / savana

Somatic structural variant caller for long-read data
Apache License 2.0
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Include savana command in vcf output #16

Closed waltergallegog closed 1 year ago

waltergallegog commented 1 year ago

Hello, I believe it would be very useful to add the command line used invoke savana with the parameters values, in the vcf file metadata. For example cuteSV and bcftools add something like:

##CommandLine="cuteSV --threads 20   --min_size 50 --max_size 1500000 --min_support 2 --max_cluster_bias_INS 100 ....  --diff_ratio_merging_DEL 0.5 aligned.bam GRCh38.d1.vd1.fa variants.vcf ."
##bcftools_viewCommand=view -i '( SVTYPE = "DEL" || SVTYPE = "INS" )' variants.vcf; Date=Wed Feb 15 00:13:40 2023

This would help when reconstructing the history of a vcf file. BR Walter

helrick commented 1 year ago

Thanks very much for your suggestion. I've implemented this in commit fdbab9c as a savana_args= field in the header which lists the command line arguments. This change will be included in the next release of SAVANA which should also address issue #17