Ditto, it is a pain also for us, would be very nice to have it fixed in GATK. They say in http://getsatisfaction.com/gsa/topic...ent_i_d_events that this is a buggy CIGAR but I doubt - there is nothing to say adjacent I/Ds are forbidden. New aligners that are not based on Smith-Waterman or BW can generate valid alignments with CIGARs like this. Should we ask them again on the GATK forum to have an other look?
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Stampy->GATK
Originally posted by ameynert View PostYes, I was using Stampy 0.1.12 to generate the alignments. The problem is fixed in Stampy 0.1.13 as far as I can tell. I've generally been pretty happy with the indels generated from a Stampy > realign > score recal > unifiedgenotyper pipeline.
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Exact same problem
I'm using version 13 of Stampy, but have exactly the same problem when trying to call indels with -glm INDEL, namely:
"SAM/BAM file SAMFileReader{/Volumes/Data/sherlock/Pseudomonas/All_PAO1_strains.realigned.recal.bam} is malformed: Adjacent I/D events in read MAGNUM:2:65:15227:4196#0"
The reads in question have the following alignments:
MAGNUM:2:65:15227:4196#0 83 NC_002516.2 33359 5 4M4D2M11I19M = 33371 -16 TGAACCGCTCTTCTGATCTCGGCGGTGTATTCGCCG =8?8=C7HAF?AF<;2=G@G:CH:3?/,4:8A1;3: RG:Z:GSRG000011 NM:i:1 MQ:i:5 OQ:Z:=7?5A@4A@BA@B:@@7D@D@BA@BB338:86868B PQ:i:431 UQ:i:23 XQ:i:228
MAGNUM:2:65:15227:4196#0 163 NC_002516.2 33371 5 18M11I6D7M = 33359 16 CGGCGGTGTATTCGCCGAGATCGGAAGAGCGTCGTG @FGEFIBKB?DBHJGHKCID=FJJ9FB9K0KCIKCB RG:Z:GSRG000011 NM:i:1 SM:i:0 MQ:i:5 OQ:Z:IHIGFGIIIDGGGEEIIBDI@DGG8G?DG2GDGGGD PQ:i:431 UQ:i:42 XQ:i:204
The file worked fine for calling SNPs. Does anyone know a fix or workaround? Can one simply:
samtools view All_PAO1_strains.realigned.recal.bam | grep -v "MAGNUM:2:65:15227:4196#0" > fixed.sam
add in the header, index and rerun? I guess I'll try.
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Originally posted by NGSfan View PostHi Gavin,
try adding -rf BadCigar and see what happens.
Let me know if it works for you
Many thanks for the help.
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Same problem--running identical pipelines on some exome data with several aligners and only got this error with the Stampy (v14) BAMs (specifically for -INDEL or -BOTH, but not with -SNPS). Will try the above--ThanksLast edited by dustinlong; 01-21-2012, 10:15 AM.
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Originally posted by dustinlong View PostSame problem--running identical pipelines on some exome data with several aligners and only got this error with the Stampy (v14) BAMs (specifically for -INDEL or -BOTH, but not with -SNPS). Will try the above--Thanks
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