So, yes, it probably states to use a .vcf file, and not a compressed version ... but if you absentmindedly just plug in a vcf.gz into a script template, everything seems to work fine because ANNOVAR can handle a .vcf.gz , but when you get to grep '#' $VCF | tail -n 1 > ${OUTFILE}.avinput.header in individual_psap_pipeline.sh, it gives an unexpected output, and then when the R script tries to read that, it errors out.
I might make a PR... bash is something I can do :)
So, yes, it probably states to use a .vcf file, and not a compressed version ... but if you absentmindedly just plug in a vcf.gz into a script template, everything seems to work fine because ANNOVAR can handle a .vcf.gz , but when you get to
grep '#' $VCF | tail -n 1 > ${OUTFILE}.avinput.headerin individual_psap_pipeline.sh, it gives an unexpected output, and then when the R script tries to read that, it errors out.I might make a PR... bash is something I can do :)