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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.