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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.2 (i.e. the second beta release) is out. See the GATK4 BETA page for download and details.

Indel calling in pooled samples

I am calling indel in pooled samples using this command:
java -jar -Xmx2g /PATH/2.1.13/GenomeAnalysisTK.jar -l INFO -T UnifiedGenotyper -I pool1.bam -I pool2.bam --out INDEL.vcf -R /reference.fa -glm INDEL

Currently i donot have any information of already known indels.
1.Do i need to first realign (RealignerTargetCreator and IndelRealigner) and then call indels even for pooled data?
2. How different will this be for calling indel on individual sample?

Looking forward for your suggesions.
with thanks sasha

Best Answers


  • sashasasha Member

    Thank you it did answer my question. In the second part i was just wondering if we have individual samples (instead of pool) then will it differ from calling indels? But i think in both cases we need to do the local realignment process (as you mentioned above).

  • sashasasha Member
    edited April 2013

    One more question related to this topic, Now that i have realigned (RealignerTargetCreator and IndelRealigner) and finally got a realigned.bam file by using this command:
    java -jar -Xmx2g /PATH/2.1.13/GenomeAnalysisTK.jar -l INFO -T IndelRealigner -I pool1.bam -I pool2.bam -I pool3.bam ... -L chr1 -targetIntervals pools_chr1.intervals -R reference.fa -o pools_realignedBam_chr1.bam

    So now i should use this pools_realignedBam_chr1.bam to call indels using:
    java -jar -Xmx2g /PATH/2.1.13/GenomeAnalysisTK.jar -l INFO -T UnifiedGenotyper -I pools_realignedBam_chr1.bam --out INDEL.vcf -R reference.fa -glm INDEL

    My question is that should i realign all pool1.bam pool2.bam … seperately? or its the right way by first realigning all pools together and then passing a single realigned file to unified genotyper??

    Looking forward for your guidance.

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