Hello Torsten,
I’ve noticed an error while running Snippy v4.6.0 that is invoking FreeBayes with the following in the final.vcf header:
##commandline="freebayes -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam --region U00096.3:0-314605"
This limits analysis to the first ~300 kb (positions 0–314 605) of my single 4.6 Mbp contig, and the resulting final.vcf is empty. How can I ensure Snippy/FreeBayes analyzes the full 4.6 Mbp contig?
Hello Torsten,
I’ve noticed an error while running Snippy v4.6.0 that is invoking FreeBayes with the following in the final.vcf header:
##commandline="freebayes -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam --region U00096.3:0-314605"
This limits analysis to the first ~300 kb (positions 0–314 605) of my single 4.6 Mbp contig, and the resulting final.vcf is empty. How can I ensure Snippy/FreeBayes analyzes the full 4.6 Mbp contig?