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.
Is it possible to source and read bam files directly from ftp site into Unified Genotyper without downloading them first. This option works in samtools view -- but if I try the simple straightforward way in GATK (just replacing the -I inputfilename.bam with -I ftplinktobamfile.bam ) it does not work. Is there another way of doing this? This would save me a lot of diskspace if I could do this.