Cannot run HaplotypeCaller in GATK

Question

[ImBioMario]

Hello! I am trying to conduct a SNP calling with HaplotypeCaller but i got an error message that theres something wrong with my *.BAM files. After checking what is wrong i got a message that my *BAM files do not have read groups. My question is how do i deal with that error? Can i add 'dummy read groups' so i could force running HaplotypeCaller? How the results would change if i would add read groups correctly? I dont quite understand the required parameters for AddOrReplaceReadGroups tool.

Here are headers of my *.BAM files (used: samtools viev -H ...):

https://pastebin.com/fdSyyfPW

https://pastebin.com/dwK9h14F

https://pastebin.com/QGwkd05X

P.S. I mapped whole human genome with 3 different tools. Raw NGS reads were pair-end reads.

Thanks in advance!

Answer 1

[Brice Sarver]

AddOrReplaceReadGroups in the Picard manual should tell you everything that you need to know. There's also a link to the GATK's definition list for more detailed explanations. You should also consider searching on Biostars - this has come up many times before.

Answer 2

[tothepoint]

java -jar /pathtopicard/AddOrReplaceReadGroups.jar I= input.bam O=output.bam RGID=4 RGLB=libx RGPL=illumina RGSM=namesample

Check this