User: merella.stefania

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Posts by merella.stefania

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Comment: C: CNVkit for germline samples
... I looked at 1294-15_S3.reference and the spread column in the BRCA1 region, values goes from 0.07 to 0.23. This are the rows in the 1294-15.reference: chromosome start end gene log2 depth gc rmask spread chr17 41197644 41197870 BRCA1 -0.233667 402. ...
written 21 hours ago by merella.stefania0
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Comment: C: CNVkit for germline samples
... Hi Eric, sorry for my late answer! 1. The panel is not an amplicon but hybrid capture. It is the Illumina trusight cancer panel. 2. Also using high value of alpha in cn_ztest.py I obtain 0 significant results, for this reason no output is created. I did again the analysis, this time us ...
written 21 hours ago by merella.stefania0
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Comment: C: CNVkit for germline samples
... Hi Eric, Many thanks for your answer. I am not using whole exome data but I have shorter sequencing panel. I tried to analyse data as you suggested creating a pooled reference using the other samples as normal samples (in total 12 samples) python3 /usr/local/cluster/bin/cnvkit.py batch germlin ...
written 7 days ago by merella.stefania0
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CNVkit for germline samples
... Dear all, I am trying to use CNVkit to detect copy number variant in my samples. My sequencing data is derived from peripheral blood so I am looking for germline copy number variants. I don't have tumor sample, only germline. I followed the suggestions of the documentation and here is the flow o ...
cnvkit next-gen targetsequencing germline written 11 days ago by merella.stefania0 • updated 10 days ago by Eric T.1.8k
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BWA on pseudo-autosomic regions
... Dear all, I have samples sequenced with Illumina TruSight One panel on a MiSeq sequencer. We are interested in variants on SHOX gene that is located on the pseudo-autosomic region on chrX and chrY. I used BWA mem for the alignments and the reference is the hg19 downloaded from UCSC: **bwa mem -t ...
variant calling alignment bwa chrx chry written 12 months ago by merella.stefania0

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