User: sichan

gravatar for sichan
sichan50
Reputation:
50
Status:
New User
Location:
Canada
Last seen:
1 year, 9 months ago
Joined:
2 years, 6 months ago
Email:
s*****@bcgsc.ca

Posts by sichan

<prev • 10 results • page 1 of 1 • next >
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Comment: C: Anyone used BAMSurgeon to spike in 1KB insertions/deletions?
... Thanks for your response, Adam.  I just sent you an email. ...
written 23 months ago by sichan50
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Anyone used BAMSurgeon to spike in 1KB insertions/deletions?
... Hi Everyone, I'm interested in using BAMSurgeon (https://github.com/adamewing/bamsurgeon/) to spike in structural variants up to 1KB in length to my BAM. Here's my command: python addsv.py -v SVs.bed -f Input_BAM -r hg19.fa -o Output_BAM > out.txt 2>error.txt Where SVs.bed contains the foll ...
genome bam bamsurgeon svs written 2.0 years ago by sichan50 • updated 7 months ago by lzy0
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Somatic indel calling with Pindel
... Hello, I noticed that Pindel was previously reported to not be able to call somatic indels without post-processing, e.g. see these posts: https://www.biostars.org/p/95166/ http://seqanswers.com/forums/showthread.php?t=42881 However, I noticed that the latest version of Pindel (0.2.5b1) has the --N ...
indels pindel somatic written 2.2 years ago by sichan50
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Comment: A: No Somatic SNV Calling with GATK?
... Thanks everyone!  Yes, I forgot to mention that I had already started running MuTect, which is also from Broad.  ...
written 2.4 years ago by sichan50
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No Somatic SNV Calling with GATK?
... Hi, I see that GATK should *not* be used to call somatic variants from tumor/normal pairs: http://gatkforums.broadinstitute.org/discussion/2405/can-i-use-unifiedgenotyper-to-call-somatic-variants-in-tumor-control-tissues Is this still true today?  I ask because someone who is no longer in our grou ...
snp written 2.4 years ago by sichan50
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Comment: C: Using SomaticSniper to call variants in specific regions?
... Looks like it's not possible with SomaticSniper: https://www.biostars.org/p/9792/#31720 ...
written 2.4 years ago by sichan50
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Using SomaticSniper to call variants in specific regions?
... Hello, I'm using SomaticSniper version 1.0.4 to call somatic variants in my tumor/normal paired BAMs.  I don't think it's possible to call SomaticSniper in a specific region in my BAMs, correct?  There doesn't seem to be an option for the user to specify a BED file for SomaticSniper to call variant ...
genome next-gen snp sequencing written 2.4 years ago by sichan50 • updated 2.4 years ago by Sean Davis23k
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Which Somatic SNP Callers to Benchmark?
... Hi Everyone, I want to benchmark somatic variant callers.  The callers should: handle tumor/normal genomes, but it would be nice if the caller could handle exomes, targeted resequencing, etc be well supported and maintained (e.g. questions/answers regarding software being posted in online forum ...
assembly next-gen snp written 2.5 years ago by sichan50 • updated 2.5 years ago by Len Trigg880
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Comment: C: Comparing Genotypes from NA12878 to that of her parents (NA12891 and NA12892)
... According to the README from Genome in a Bottle, the VCF contains highly confident hetero- and homozygous variant calls, thus implying that those variants are in highly confident regions.   Any position in the confident BED file but not the VCF can be confidently treated as homozygous reference. ft ...
written 2.5 years ago by sichan50
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Comparing Genotypes from NA12878 to that of her parents (NA12891 and NA12892)
... Hello, I'm interested in comparing the genotypes from Genome in a Bottle's NA12878 (GIAB) to those of her parents (NA12891 and NA12892). I downloaded GIAB's NA12878 vcf from here: ftp://ftp-trace.ncbi.nih.gov/giab/ftp/release/NA12878_HG001/latest/NIST_RTG_PlatGen_merged_highconfidence_v0.2_Allanno ...
genome next-gen snp written 2.6 years ago by sichan50 • updated 2.5 years ago by Len Trigg880

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