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GATK4: 1 sample / 1 Library / 4 Lanes

manolismanolis Member ✭✭

Hi, if possible I would like to have a confirmation:

I have 8 fastq (2 fastq per lane, R1 and R2) data from 1 sample, prepared as 1 library and ran in 4 different lanes (1,2,3,4).

Looking in the forum and yours blogs I made a pipeline. Could you tell me if is it correct?

All pre-processing steps were ran per lane fastq. Before HaplotypeCaller I done a step with AddOrReplaceReadGroups in each bam (4 bam):

java -jar ${PICARD} AddOrReplaceReadGroups I=${input} O=${output} RGSM=${newSM} RGLB=${LB} RGPL=${PL} RGPU=${PU}

In this way I have the same RG for all bam files. The variables "newSM";"LB" ;"PL";"PU" are the same for all 4 bam.

At HaplotypeCaller step I used as input files all 4 bam files.

Could create any problem this pipeline at MarkDuplicate and BQSR level? I think no but please let me know.

Many thanks.

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