
Laurent MANCHON
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Latest activity by Laurent MANCHON-
Laurent MANCHON commented,
in the same way for the X chromosome of the male individual. Whereas for the other chromosomes the normality threshold is 2.
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Laurent MANCHON commented,
so CNVs on the Y chromosome that are greater than 1 will be considered as DUPs and those less than 1 as DELs.
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Laurent MANCHON commented,
Yes, but the ploidy calculation for male individuals is not the same. Is the CNV on the Y halved?
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Laurent MANCHON commented,
Hi, Do i need to use a PON of male samples or female samples ? And i use a PON of male samples do i need to cut in half the CNV on Y and X ? Thank you --
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Laurent MANCHON commented,
yes, i known.But it works fine with past version of GATK, so, my solution was to use version 4.2.6.1 with R-3.6.2
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Laurent MANCHON created a post,
problem with R library
REQUIRED for all errors and issues: a) GATK version used:4.4b) Exact command used: module load Python-3.11.1 java.17.0.6module load R.4.3.0 # with getopt_1.20.0 and optparse_1.3.2 gatk --java-optio...
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Laurent MANCHON commented,
for now this problem is over for me because i have added those parameters to Mutect2: --read-filter NotSecondaryAlignmentReadFilter \--read-filter NotSupplementaryAlignmentReadFilter \--interval-pa...
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Laurent MANCHON commented,
no.this is the command i use: bwa-mem2 mem -M -w 150 -d 80 -c 2000 -t 24 -R "@RG\tID:${lib}\tSM:${lib}\tLB:${lib}\tPL:ILLUMINA" $GENOME/GRCh38_p13.fa $f1 $f2 | samtools fixmate -O bam -@ 24 - - | s...
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Laurent MANCHON commented,
i have only a tumor bam file and a pon.hdf5 and no normal libraryIs it possible to use this pipeline ?I'm looking for a bash pipeline with all the GATK commands to find the CNV, is it available som...
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Laurent MANCHON commented,
that's what I did in my analysis, I used the genome GRCh38_p13 (08.2022) from gencode consortium. I have removed all the alts contigs and use only the chromosome sequences.