GATK BaseRecalibrator error

[craigledee]

Hi,

I posted this in the GATK forum, but will try here too- I'm catching an error with BaseRecalibrator that might require me to use the old CIGAR format (). I'm using the first-pass high-coverage parental calls for the knownSites argument. Can anyone suggest a work around?

Thanks!


java -Xmx60g -jar /apps/gatk/3.2.0/GenomeAnalysisTK.jar -l INFO -R /flush1/and48y/genomic_resources/all-chr-r.fasta -T BaseRecalibrator -I GR_F_realignedBam.bam -knownSites GR_parent_DP10_ref.vcf -o recal_data_GR.table

ERROR stack trace
org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException: BUG: Unexpected CIGAR element htsjdk.samtools.CigarElement@655936aAG_TATCCTCT

samtools view GR_F_realignedBam.bam | grep FCC4THYACXX:2:1216:16584:2572#CGTACTAG_TATCCTCT

FCC4THYACXX:2:1216:16584:2572#CGTACTAG_TATCCTCT 113 HaChr01 1 25 6S8X1=2X67=1X5= HaChr21 116043 0 ATGTGTATAAGAGACAGGCTTTAAACCATACAATGAACGCTTTAAGAGACAGGCATCTCCTCCAGCTTGAAGATCCACTAACATATTATT CEC@FFFFFFFHECCEIIGEHAIHHIHEIHGJIDJHEJIIGGIJIIJIGJIJJJIGGBJIEJIIJJJJJJJJJIJHGHHHHHFFFFFCCCPG:Z:MarkDuplicates RG:Z:GR_F AM:i:25 NM:i:17

[Brian Bushnell]

Was that generated by BBMap? You can force it to output in the old format with the "sam=1.3" flag. Otherwise... theoretically, if you parsed the sam file, and just altered the cigar strings to replace "=" and "X" with "M", it might work. In sam format you're not supposed to have a string with identical adjacent operators like "8M4M12M", but the parsers I've written won't complain about that - possibly, GATK would accept it.