after running gimble parse, gimble.vcf.gz is null

[kuangzhuoran]

my command is gimbleprep -f ./galili.fa -b ./galili.bam -v ./galili.golani.rename.vcf.gz -k -t 40

[GertjanBisschop]

Thanks @kuangzhuoran for reporting this. Could you provide a bit more information so we can try and reproduce the error?

Note though that the -b flag should be followed by a directory of bam files, not an actual bam file.

[kuangzhuoran]

gimble.log.txt

[kuangzhuoran]

Thanks for the reply, the -b parameter follows a folder。 Do I need to take a portion of the input file and send it to you. I have now uploaded the log file

[kuangzhuoran]

I used gatk to extract the SNPs, but it was running successfully before. bam file is using sambaba to remove PCR duplicates!

[GertjanBisschop]

Can you be more specific about gimble.vcf.gz is null? What does the output look like? Obviously, gimbleprep is a filtering step. Is it possible that after applying filters there are no more SNPs left?

[kuangzhuoran]

Only the header

[kuangzhuoran]

“Is it possible that after applying filters there are no more SNPs left”

It's possible.