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Issues with combining VCF

mforde84mforde84 chicagoMember
edited July 2015 in Ask the GATK team

I used a pipeline created by a different person which at one point or another was considered "best practice" according to GATK standards:

java -jar $gatk -T HaplotypeCaller -R $ref_fa -I $file -o $file".HC.SNP.INDEL.vcf" -rf BadCigar;

However, when I try to aggregate these calls across 2-3K samples using HC or combinegVCF I get the following error:

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 3.3-0-g37228af):
ERROR
ERROR This means that one or more arguments or inputs in your command are incorrect.
ERROR The error message below tells you what is the problem.
ERROR
ERROR If the problem is an invalid argument, please check the online documentation guide
ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
ERROR
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
ERROR
ERROR MESSAGE: The list of input alleles must contain as an allele but that is not the case at position 150; please use the Haplotype Caller with gVCF output to generate appropriate records
ERROR ------------------------------------------------------------------------------------------

and results from the very first call:

CHROM POS ID REF ALT QUAL FILTER INFO

chrM 150 . T C 107.28 . AC=2;AF=1.00;AN=2;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.83;SOR=1.179

your guide suggests that i recall every single bam file! and i think that's particularly insane. so my question is simply this ... why?

Answers

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