freebayes: changing min-coverage setting and still getting same size file output

Question

[laurenvw]

Hi all,

I'm trying to run freebayes with a few different coverage options to compare how many variants are called. I want to try a --min-coverage of 5, 7 and 10, but when I run these codes, I get a file of the same size generated for all three. Shouldn't I expect them to be drastically different? The min-coverage threshold is the only parameter I change between the runs, so it seems like the problem must be there. Has anyone run into a similar problem or have any ideas as to what might be happening? Here is my code:

~/dDocent/freebayes/bin/freebayes -f reference50.fasta -0 -E 3 -F .2 -G 10 -z .1 -X -u -n 2 --populations poplist.txt --min-coverage 10 --min-repeat-entropy 1 -V -b cat_sortMq10_realigned.bam -v cat_sortMq10_fbraw_mincov10_n2_poplist.vcf

Lauren

Answer 1

[apelin20]

1. Try grep -v file.vcf | wc -l for both files, prints amount of variants called.
2. If your coverage is generally above 10, changing mincov to 5 7 shouldn't change results much.