If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Why are some indels being called when in the read mapping there are none?
I have found some INDELS called that are not present in the read mapping and dont understand why it might happen or how to solve it.
I have tried to the calling with and without indel recalibration of the reads, but in both cases the same behaviour occurs.
The commands I have used are:
java -jar /source_installers/GenomeAnalysisTK.jar -T HaplotypeCaller -R ../../SNPS/503.fasta -I EfmD8t72_hdr.bam -o EfmD8t72_gatk_norecal.vcf
java -Xmx2g -jar /source_installers/GenomeAnalysisTK.jar -T RealignerTargetCreator -R ../../SNPS/503.fasta -I EfmD8t72_hdr.bam -o EfmD8t72.intervals
java -Xmx4g -jar /source_installers/GenomeAnalysisTK.jar -T IndelRealigner -R ../../SNPS/503.fasta -I EfmD8t72_hdr.bam -targetIntervals EfmD8t72.intervals -o EfmD8t72_realigned.bam
java -jar /source_installers/GenomeAnalysisTK.jar -T HaplotypeCaller -R ../../SNPS/503.fasta -I EfmD8t72_realigned.bam -o EfmD8t72_gatk.vcf
The results I mentioned are:
gi|403040827|gb|AMBN01000124.1| 6975 . C CAG 7789.73 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.598;ClippingRankSum=0.000;DP=197;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.04;MQRankSum=0.000;QD=32.80;ReadPosRankSum=1.735;SOR=0.313 GT:AD:DP:GQ:PL 1/1:1,175:176:99:7827,485,0
gi|403040827|gb|AMBN01000124.1| 6977 . ACC A 7780.73 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.567;ClippingRankSum=0.000;DP=197;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.04;MQRankSum=0.000;QD=28.26;ReadPosRankSum=1.706;SOR=0.313 GT:AD:DP:GQ:PL 1/1:1,175:176:99:7818,485,0
The mapping of the reads as shown by CLC Genomics:
Also similar results happened in other regions of the same mapping.