How can i edit some rows in .bam header file? - BioStar

How can i edit some rows in .bam header file? - BioStar

Question: How can i edit some rows in .bam header file?
2	For example i have the following already in the bam header: @RG ID:110131_SN107_0398_A81DDCABXX_LANE2 PL:ILLUMINA LB:P0007 SM:tumor @RG ID:110131_SN107_0398_A81DDCABXX_LANE4 PL:ILLUMINA LB:P0007 SM:tumor @RG ID:110131_SN107_0398_A81DDCABXX_LANE6 PL:ILLUMINA LB:P0007 SM:tumor @RG ID:110131_SN107_0398_A81DDCABXX_LANE8 PL:ILLUMINA LB:P0007 SM:tumor @RG ID:110131_SN107_0399_B81CYUABXX_LANE2 PL:ILLUMINA LB:P0007 SM:tumor @RG ID:110131_SN107_0399_B81CYUABXX_LANE4 PL:ILLUMINA LB:P0007 SM:tumor @RG ID:110131_SN107_0399_B81CYUABXX_LANE6 PL:ILLUMINA LB:P0007 SM:tumor @RG ID:110131_SN107_0399_B81CYUABXX_LANE8 PL:ILLUMINA LB:P0007 SM:tumor i want to make it: @RG ID:110131_SN107_0398_A81DDCABXX_LANE2 PL:ILLUMINA LB:tumor_P0007 SM:tumor @RG ID:110131_SN107_0398_A81DDCABXX_LANE4 PL:ILLUMINA LB:tumor_P0007 SM:tumor @RG ID:110131_SN107_0398_A81DDCABXX_LANE6 PL:ILLUMINA LB:tumor_P0007 SM:tumor @RG ID:110131_SN107_0398_A81DDCABXX_LANE8 PL:ILLUMINA LB:tumor_P0007 SM:tumor @RG ID:110131_SN107_0399_B81CYUABXX_LANE2 PL:ILLUMINA LB:tumor_P0007 SM:tumor @RG ID:110131_SN107_0399_B81CYUABXX_LANE4 PL:ILLUMINA LB:tumor_P0007 SM:tumor @RG ID:110131_SN107_0399_B81CYUABXX_LANE6 PL:ILLUMINA LB:tumor_P0007 SM:tumor @RG ID:110131_SN107_0399_B81CYUABXX_LANE8 PL:ILLUMINA LB:tumor_P0007 SM:tumor Thanks. samtools bam	created 10 months ago by Hmm   24•8 last edit by Lars Juhl Jensen ♦
	similar posts • permalink • log in to comment • revisions

1 answer

12	samtools view -H mybamfile.bam | sed -e 's/LB:/LB:tumor_/' | samtools reheader - mybamfile.bam > mybamfile.reheadered.bam