Dina Tzur
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Activity overview
Latest activity by Dina Tzur-
Dina Tzur commented,
Hi Genevieve Brandt, Thanks! Dinna
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Dina Tzur commented,
In addition, I ran HaplotypeCaller once more on the same file and received a different output file from previous times. A much larger file ..
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Dina Tzur created a post,
WARN InbreedingCoeff - InbreedingCoeff will not be calculated at position chr1:40 and possibly subsequent; at least 10 samples must have called genotypes
Answereda) GATK version used: GATK 4 b) Exact command used: gatk HaplotypeCaller -R $(GENOME_file_LAB) -I $(FILE).ao.sort.bam -O $(FILE).raw_variants_help.vcf; \ Hi, I would love to help. I ran the GAT...
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Dina Tzur commented,
Thank you! Dina
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Dina Tzur commented,
Hi Genevieve, Thank you very much!So it seems that MARKDUPLICATE works well for me? Dina
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Dina Tzur commented,
Hi Genevieve, The truth is that I have run the MARKDUPLICATE already once on the files and got a matrix in this style: ## htsjdk.samtools.metrics.StringHeader# MarkDuplicates INPUT=[/sci/home/d...
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Dina Tzur commented,
And the matrix I get: ## htsjdk.samtools.metrics.StringHeader# MarkDuplicates INPUT=[/group/BAM_z/BAM_Lee2013/bam_bai/2.0hpf_wt_total.star.bam.sort.bam] OUTPUT=/group/BAM_z/BAM_Lee2013/md/2.0hpf_wt...
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Dina Tzur commented,
[bam_sort_core] merging from 10 files and 1 in-memory blocks...INFO 2022-02-16 21:09:14 MarkDuplicates ********** NOTE: Picard's command line syntax is changing.******************** For more...
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Dina Tzur commented,
Hi Genevieve Brandt, Thanks for the attention! Can you explain to me how I find it? Thanks again! Dina
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Dina Tzur created a post,
AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '<optimized capture of last three': 'separated fields as numeric values>' did not match read name '2hpf_wt_total_SRR870747.42096'.
AnsweredGATK version used: GATK4 I tried to run MarkDuplicates like this: picard MarkDuplicates I = $ (FILE) .sort.bam O = $ (FILE) .MD.bam M = $ (FILE) .MD_matrix.txt; And I got the comment: WARNING 2022...