I have tried to implement sequenza-utils on conda env (python 3.8)
Command is "sequenza-utils snp2seqz --vcf strelka_somatic_snvs.vcf -gc hg19_gc50.wig.gz --preset strelka2_som --output GA060TP95.som.seqz.gz"
1.Then, I encountered "map is not subscriptable" in sequenza/vcf.py parse_strelka2_som function (In this part, we can check .somatic.snvs.vcf from Strelka2 is used in sequenza). so, I modified map(int, ~~~) to list(map(int,~~~))
2.Different contig names in between .vcf files and wig files cause empty seqz.gz file. based on what is the difference between GRCh37 and hg19 ?, I modified vcf.py to fit contig names to hg19 (e.g. "1" to "chr1" for 1-22, X, and Y chromosomes)
Finally, fixed. I hope this reports will be helpful to estimate tumor purity from Strelka output on python3.8
p.s. when I read source code, vcf.py "sequenza-utils" uses Tier 2 allele depth from Strelka 2 pipeline. Is it reasonable?
