User: erarroji

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erarroji0
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Posts by erarroji

<prev • 7 results • page 1 of 1 • next >
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Comment: C: Trouble with best practices
... Thank you, I will trust GATK. The variant calling was made with the same tool (Mutect 2), I only changed the markduplicates tools. In all cases y used default values, could that be what is generating troubles? ...
written 4 months ago by erarroji0
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Comment: C: Trouble with best practices
... Thank you, I did checked the duplicates, they were as fraction and also I checked it with samtools flagstat making the calculation with the raw values. ...
written 4 months ago by erarroji0
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Trouble with best practices
... Hi I'am new with all NGS tools, I tried to follow best practices workflow for my exome reads from tumor samples: I align with bwa mem, sort with samtools, mark duplicates and recalibrated bases with GATK 4 and finally call variants with Mutect 2. Although the software run successfully I noticed tha ...
bioinformatics ngs wes samtools gatk written 4 months ago by erarroji0
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Comment: C: Picard CollectHsMetrics malfunctioning
... I really thank you it has been really useful ...
written 6 months ago by erarroji0
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Comment: C: Picard CollectHsMetrics malfunctioning
... Already did. Coverage depth, mean coverage and off target. ...
written 6 months ago by erarroji0
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Comment: C: Picard CollectHsMetrics malfunctioning
... Thank you Pierre, i've been struggling with this all week. It is exactly the same mistake, but my input files are ok. Could you suggest me another software for calculate the metrics? Thank you ...
written 6 months ago by erarroji0
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Picard CollectHsMetrics malfunctioning
... I tried to run CollectHsMetrics, this is my command: java -jar /picard.jar CollectHsMetrics \ I=190.sortedDeDup.bam \ O=190_hs_metrics.txt \ R=ucsc.hg19.fasta \ BAIT_INTERVALS=AgilentSSV6_bait_list.interval_list \ TARGET_INTERVALS=V6SureSelect/AgilentSSV6_targets_list.interval_list it works ok unt ...
picard ngs wes collecthsmetrics written 6 months ago by erarroji0 • updated 6 months ago by Pierre Lindenbaum108k

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