If you happen to see a question you know the answer to, please do chime in and help your fellow community members. 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.
BAMs with multiple RG lines
I have a set of BAMs, of them most contains multiple RG lines (same sample were run multiple times sequencing).
Now I need to run GATK HC caller (the BAM-> g.vcf -> vcf route), it complains that:
ERROR MESSAGE: Invalid command line: Argument emitRefConfidence has a bad value: Can only be used in single sample mode currently. Use the sample_name argument to run on a single sample out of a multi-sample BAM file.
The command I used:
java -XX:ParallelGCThreads=4 -Xms10g -Xmx10g -Djava.io.tmpdir=/scratch_space \
-jar GenomeAnalysisTK.jar -T HaplotypeCaller \
-R GRCh37-lite.fa --emitRefConfidence GVCF \
--variant_index_type LINEAR --variant_index_parameter 128000 \
--dbsnp dbsnp_138.b37.vcf -I input.bam -L 4 \
I am guessing if I provide the following parameter it will run the that sample ONLY?
What would be the easiest way to get around this? I know that I can
- use picard to modify the RG tag, generating new BAMs
- any other ways to get haplotypecaller run?