We've moved!
This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!

Error while running BaseRecalibrator

Hello, I was running the BQSR on the RNAseq reads. This is the command i typed:

java -jar /usr/local/bin/GenomeAnalysisTK.jar -T BaseRecalibrator -R ../../../genome/hg38/hg38.fa -I a_split.bam -L 22 -knownSites ../../../genome/vcf/All_20170710.vcf -o a_sorted.bam_dedupped_split_recal_data.table

However, I get this error:
ERROR MESSAGE: The platform (platform) associated with read group GATKSAMReadGroupRecord @RG:id is not a recognized platform. Allowable options are ILLUMINA,SLX,SOLEXA,SOLID,454,LS454,COMPLETE,PACBIO,IONTORRENT,CAPILLARY,HELICOS,UNKNOWN.

I used the sed command to change the PL:platform to PL:SOLID using this command:

samtools view -H a_split.bam|sed -e 's/PL:platform/PL:/g'|samtools reheader - a_split.bam >a_reheadered.bam

But I then get another error stating that the BAM file is not indexed. How is changing one line in the header make it unindexed? Can anyone comment on this.



Best Answer


Sign In or Register to comment.