Nguyen Nguyen Thanh
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Activity overview
Latest activity by Nguyen Nguyen Thanh-
Nguyen Nguyen Thanh created a post,
HaplotypeCaller: java.lang.NullPointerException
a) GATK version used: 4.1.4.1b) Exact GATK commands used: gatk HaplotypeCaller -I NA12878.final.cram -O NA12878.final.vcf -R GRCh38_full_analysis_set_plus_decoy_hla.fa -L vdj_hg38.bed c) The entire...
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Nguyen Nguyen Thanh commented,
I have tried two cases using Sort by queryname: 1, Sorting unmapped file then MergeAlignment INFO 2020-02-25 12:13:30 SamAlignmentMerger Processing SAM file(s): [aln/HG01842.mapped.ILLU...
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Nguyen Nguyen Thanh commented,
I have run CountReads on both file and they return the same counts. For ValidateSamFile, I use this command for both file: java -jar $PICARD ValidateSamFile I=HG02142.mapped.ILLUMINA.bwa.KHV.low_co...
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Nguyen Nguyen Thanh created a post,
Question: Picard - MergeBamAlignment: Reads remaining on alignment iterator
Hi, I'm new to genome analysis and I need some advice on this. I'm currently follow GATK best practice, now I'm stuck at the MergeBamAlignment step of picard. I'm using the data from https://www.in...