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I finally found what was wrong, I just didn't run ReorderSam on my bam file. After I did that, GATK ran like a charm ! Thanks for the reply. David S.
Without -U ALLOW_SEQ_DICT_INCOMPATIBILITY I get: ERROR MESSAGE: Lexicographically sorted human genome sequence detected in reads. I run GATK 3.7-0-gcfedb67. David S.
Hello, After sorting my dbsnp vcf file as you suggested to I am still facing troubles with HaplotypeCaller as it throws the error message: ERROR -- ERROR stack trace java.lang.IllegalStateException: Rod span chr1:1-249250621 isn't contained with…