
Adi Abuali
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Activity overview
Latest activity by Adi Abuali-
Adi Abuali commented,
Thank you for the advise...Appreciated.
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Adi Abuali commented,
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 ?
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Adi Abuali commented,
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
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Adi Abuali commented,
Thank you SkyWarrior...
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Adi Abuali commented,
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...
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Adi Abuali created a post,
At which stage family genotype posterior recommened in germline discovery best practice?
AnsweredI have 4 samples (Father, Mother, son, grandson), and am trying to refine the calling using family.ped using CalculateGenotypePosteriors, and also referring to https://gatk.broadinstitute.org/hc/e...
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Adi Abuali commented,
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...
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Adi Abuali commented,
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 --...
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Adi Abuali created a post,
picard MarkIlluminaAdapters for Non-Illumina Adapters Error
Hi, When I try MarkIlluminaAdapters for Non-Illumina Adapters, it gives me below error.....Any help in correct syntax? a) GATK version used: 4.2.0 Picard Version:2.25.0b) Exact command used: picar...
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Adi Abuali created a post,
MGI DNBSEQ-T7 DNA Sequencer (Nebula) ….Is it Compatible with GATK Best Practice Pipeline?
AnsweredIf you are seeing an error, please provide(REQUIRED) : a) GATK version used: b) Exact command used: c) Entire error log: If not an error, choose a category for your question(REQUIRED):a)How do I (....