Atal Saha
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Latest activity by Atal Saha-
Atal Saha commented,
Thanks again, David. Re-calling started. cheers Atal
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Atal Saha commented,
Thanks very much, David. I did manage to produce all my vcf files. Seemed using 20-30 gb memory was a good solution. However, I accidentally did not include -ERC GVCF option while running haploty...
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Atal Saha commented,
Hi David, Thanks very much for your reply on this. Running Spark version was much faster, but I am worried about warning about this version (as it says that we should not use spark if we care about...
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Atal Saha commented,
Hi Wondessen Ayalew, Did you get any support on this? I am having the same problem - it took a week to finish generating g.vcf for 1 sample. The command I used: /gpfs/gpfs0/software/rhel7/eucleia/g...
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Atal Saha commented,
Thanks again, Louis! Answer to your questions: 1. it was silent exit with no clear error 2. Its monkfish data, whole genomes 3. inputs sorted by coordinates I have just given it up with Spark, as i...
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Atal Saha commented,
Hi Louis, Thanks for your reply on this. The problem was initially solved by increasing Xmx20g to Xmx160g. However, my files are around 20GB each (and 60files in total) and so taking forever to fin...
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Atal Saha created a post,
Markduplicates
Hi, I am trying to mark duplicates using the following command: java -Xmx20g -jar /software/eucleia/Picard_v2.27.1/picard.jar MarkDuplicates INPUT=Sample_10-LOP-083.bam VALIDATION_STRINGENCY=LENI...