Dear Geraldine, and Sheila,
a very simple question, if I may : given a VCF file from MUTECt1 or MUTECt2, how shall I split the file into 2 parts : a file with the "PASS" variants, and another file with all the other variants ?
thanks a lot,
You can use SelectVariants with --excludeFiltered and --discordance.
thank you, Sheila
If i may add another question about combining the variants : we are running MUTECT1 and MUTECT2 per chromosome, and at the end we combine the vcf files by using CombineVariants. However this produces additional columns in the vcf files that are not absolutely needed, as the samples derive from the same person. If there a way where we can just simply concatenate the VCF files with a GATK walker ? many many thanks !
aha, I could use : https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_CatVariants.php