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.
Indelrealigner creates odd CIGAR
I'm realigning around indels with GATK v2.7.4 and in one case It's causing in one instance to align my 100 bases read long as only insertions (100I)
This might be related to another thread here but the error is slightly different.
I've uploaded the test bam files before and after realignment to your ftp
Here are the command I used to realign:
java -Xmx8G -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -I test_sorted.bam -o test_sorted.intervals -R ucsc.hg19.fasta -known 1000G_phase1.indels.hg19.vcf -known Mills_and_1000G_gold_standard.indels.hg19.vcf
java -Xmx8G -jar GenomeAnalysisTK.jar -T IndelRealigner -I test_sorted.bam --out test_sorted_realigned.bam -targetIntervals test_sorted.intervals -R ucsc.hg19.fasta -known 1000G_phase1.indels.hg19.vcf -known Mills_and_1000G_gold_standard.indels.hg19.vcf