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Picard 2.10.4 has MAJOR CHANGES that impact throughput of pipelines. Default compression is now 1 instead of 5, and Picard now handles compressed data with the Intel Deflator/Inflator instead of JDK.
GATK version 4.beta.3 (i.e. the third beta release) is out. See the github release page for download and details.

heterozygous indel bug in GATK 2.4-9

Dear GATK team,

I think I found a bug as shown in the attached screenshot. The highlighted line of the vcf file after using UnifiedGenotyper, VariantRecalibrator, ApplyRecalibration, ReadBackedPhasing, SelectVariants, CombineVariants, and SnpEff (following Best Practices) shows
X 307897 . C CGTGAAGG 9494.14 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=8.010;DP=18;EFF=DOWNSTREAM(MODIFIER||||PPP2R3B|protein_coding|CODING|ENST00000381625|),INTRON(MODIFIER||||PPP2R3B|protein_coding|CODING|ENST00000390665|4),INTRON(MODIFIER||||PPP2R3B|retained_intron|CODING|ENST00000445792|5),INTRON(MODIFIER||||PPP2R3B|retained_intron|CODING|ENST00000475859|2),INTRON(MODIFIER||||PPP2R3B|retained_intron|CODING|ENST00000477110|1),INTRON(MODIFIER||||PPP2R3B|retained_intron|CODING|ENST00000496630|3),UPSTREAM(MODIFIER||||PPP2R3B|retained_intron|CODING|ENST00000468169|),UPSTREAM(MODIFIER||||PPP2R3B|retained_intron|CODING|ENST00000477636|),UPSTREAM(MODIFIER||||PPP2R3B|retained_intron|CODING|ENST00000484364|);FS=0.000;InbreedingCoeff=0.3019;MQ=45.55;MQ0=0;MQRankSum=-8.092;QD=9.55;ReadPosRankSum=2.020;VQSLOD=2.27;culprit=ReadPosRankSum;set=29_BOTH GT:AD:DP:GQ:PL ./. 0/1:0,14:9:99:367,42,0

To be sure, I checked the two samples' bams at the PrintReads stage but do not see such a long indel.
Is this a potentially similar bug to ?

Thank you for your attention.


Screenshot from 2013-04-24 16:36:26.png
1440 x 900 - 302K


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