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CommentsRecent activity by Adi Abuali Sort by recent activity
Thank you for the advise...Appreciated.
Thank you SkyWarrior...I know it's not GATK tool as well, but if you advice for MGI fastp tool as well for same approach ?
What BWA MEM parameters used in this pipleline (e.g. -M, -a,..etc.)? -M mark shorter split hits as secondary -a output all alignments for SE or unpaired PE
Thank you SkyWarrior...
In case of unaligned BAM (with --align parameter), Will this ReadsPipelineSpark follow the below process (Namely the MergeBamAlignment to include the tags, RG, UQ, MC, and MQ): https://gatk.broadi...
Finally it works with below syntax: gatk MarkIlluminaAdapters I=/mnt/d/gen/uAdi.bam O=/mnt/d/gen/uAdi.bam_mark.bam M=/mnt/d/gen/metrics.txt ADAPTERS=null FIVE_PRIME_ADAPTER=AAGTCGGATCGTAGCCATGTCGTT...
Hi Genevieve, Thanks but I tried this before and it gave me different error as below: picard MarkIlluminaAdapters -I /mnt/d/gen/uAdi.bam -O /mnt/d/gen/uAdi.bam_mark.bam -M /mnt/d/gen/metrics.txt --...