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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.