bug: contig mode does not find all snps

[Saarkie]

Hi, I'm using snippy v4.6.0 in the --ctg contig mode. It does not detect snps at the ends of the contigs. Something seems to be wrong with the uniform coverage of the pseudo reads. The coverage is rather in a mountain shape. Therefore at the ends, where the coverage is <10 the variants are not called by freebayes. If I set --mincov 1 it conflicts with the default -C 2 (min alternate count) option of freebayes. The option --fbopt "-C 1" is not parsed to freebayes correctly, the -C flag occurs two times in the command then (freebayes-parallel reference/ref.txt 8 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 2 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -C 1 -f reference/ref.fa AS164896.1_foptC1.bam > AS164896.1_foptC1.raw.vcf). If I set --mincov higher than 1, the actual coverage sometimes is smaller then the --mincov, so at this sites the variants are not called.

My "contigs" are gene sequences of ~1000bp, one sequence per separate fasta. I use it the following: $ snippy --prefix xxx --outdir xxx --ref x.gb --ctgs genex.fasta

regards, Sara