Tagged with #input
0 documentation articles | 0 events or announcements | 1 forum discussion

There are 4 comments on this article. To see them or add your own, read this post on the forum

Hello, I am a first-time user of GATK and have spent some time now on trying to get the input bam files in the appropriate format. To run IndelRealigner, I have added ReadGroups, Reordered and Index my bam file with the respective Picard-Tools.

My command-line is the following:

java -Djava.io.tmpdir='pwd'/tmp -jar GenomeAnalysisTK.jar -I ./add_read_groups_reorder_index.bam -R ./genome.fa -T IndelRealigner -targetIntervals ./gatk.intervals -o ./*.bam -known ./Mills-1000G-indels.vcf --consensusDeterminationModel KNOWNS_ONLY -LOD 0.4

I get the following message:

SAM/BAM file /home/gp53/tophat2-merge-ctl-1st-2nd-readgroups-reorder-index.bam is malformed: SAM file doesn't have any read groups defined in the header.

My reads are paired-end aligned with TopHat2 I will appreciate your help on this. Thanks, G.

There are 4 comments on this article. To see them or add your own, read this post on the forum