User: merella.stefania

Reputation:
0
Status:
New User
Last seen:
1 day, 14 hours ago
Joined:
1 year, 2 months ago
Email:
m***************@hsr.it

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by merella.stefania

<prev • 8 results • page 1 of 1 • next >
0
votes
1
answer
261
views
1
answers
Comment: C: CNVkit for germline samples
... Hi Eric, Even in this case the z-test result is 0: [smerella@srv2-slim cnvkit_brca]$ python3 ../cnvkit-master/scripts/cn_ztest.py cnvkit_brca/1294-15_S3_RGSorted.cnr -s 1294-15_S3.calls.cns -t -a 0.9 -o cnvkit_brca/1294-15_S3_RGSorted.ztest.cnr Ignoring 15118 off-target bins Significant ...
written 6 weeks ago by merella.stefania0
0
votes
1
answer
261
views
1
answers
Comment: C: CNVkit for germline samples
... Hi Eric, I aligned my samples to another reference, 1000G phase 3 (hs37d5), and I also applied BAM recalibration as suggested by GATK. In the end I applied the commands for cnvkit as I described above. The results are not so different from the others obtained before. Here is the new scatter https: ...
written 6 weeks ago by merella.stefania0
0
votes
1
answer
261
views
1
answers
Comment: C: CNVkit for germline samples
... Hi Eric, here is the link of the scatter plot. I hope it now works. https://ibb.co/d1Km1G Here is the bin in the sample.cnr file chromosome start end gene depth log2 weight chr17 41197644 41197870 BRCA1 439.704 -0.122365 0.719729 As you can see the log2 ...
written 6 weeks ago by merella.stefania0
0
votes
1
answer
261
views
1
answers
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 7 weeks ago by merella.stefania0
0
votes
1
answer
261
views
1
answers
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 7 weeks ago by merella.stefania0
0
votes
1
answer
261
views
1
answers
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 8 weeks ago by merella.stefania0
0
votes
1
answer
261
views
1
answer
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 9 weeks ago by merella.stefania0 • updated 9 weeks ago by Eric T.1.9k
0
votes
0
answers
425
views
0
answers
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 14 months ago by merella.stefania0

Latest awards to merella.stefania

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 568 users visited in the last hour