How to get five columns of vaf data for sciclone

[xiaoquexingchen]

Hi:
I may be new to bioinformatics, and I don’t know much about some knowledge. I now have matched bam files and vcf files. How can I use these data to get the five-column vaf data required by sciclone? There is also the copy number. Can these files be omitted when running sciclone in LOH? Looking forward to your reply, thank you very much!

[chrisamiller]

If you have VCF files, you may or may not already have what you need. For somatic calling, these are often stored in Allelic Depth(AD) and Allelic Fraction (AF) fields in the VCF. If not, you can use bam-readcount to add this information. One example of how to do this is here: https://pvactools.readthedocs.io/en/latest/pvacseq/input_file_prep/readcounts.html Copy number can be called by many different algorithms - CNVkit is one that we've had good luck with in the past. Best of luck