AddOrReplace gp in Pickard Sam validation error

Question

[KG]

I performed Indexing and alignment RNA seq with ref genome everything worked fine. then convert cooordinate (convert coordinates basically takes the reads that map onto the splice junctions and “remaps” them onto the canonical chromosomes.) before I was going to picard markduplicate step it was throwing error can not write to sam dictioary and found that to resolve this issue is to Apply AddOrReplace readgps . However now I am getting an error for this step also: samtools samtool format exception sam validation error: Error: Record 13, readname K00193:38:h3myfbbxx:4:1101:10043:46568, mark should be 0 for unmapped read.

and the command i used

java -jar picard.jar AddOrReplaceReadGroups \ 
    INPUT=reads.bam \ 
    OUTPUT=reads_addRG.bam \ 
    RGID=H0164.2 \ #be sure to change from default of 1
    RGLB= library1 \ 
    RGPL=illumina \ 
    RGPU=H0164ALXX140820.2 \ 
    RGSM=sample1 \

Please help me with this how to resolve. Thanks a lot in advance

Answer 1

[Pierre Lindenbaum]

add

VALIDATION_STRINGENCY=LENIENT

[KG]

Thanks a lot it worked

[KG]

Thanks! This worked for me.