User: Amitm

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Amitm1.6k
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Posts by Amitm

<prev • 224 results • page 1 of 23 • next >
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Comment: C: faster variant annotation for large VCFs
... Thanks again. With 2x the buffer size than default and n=16 threads the process completed in ~7hrs! ...
written 4 months ago by Amitm1.6k
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Comment: C: faster variant annotation for large VCFs
... Hi, Have you been able to make it work? After installing VEP, you need to have run - perl \ INSTALL.pl \ --AUTO p \ --PLUGINS CADD,ExAC \ --SPECIES homo_sapiens_merged \ --ASSEMBLY GRCh37 That would configure the plugins (you specify) under the vep data cache Plugins/ path. ...
written 4 months ago by Amitm1.6k
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Comment: C: faster variant annotation for large VCFs
... many thanks! Going to try this ...
written 4 months ago by Amitm1.6k
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faster variant annotation for large VCFs
... hi there, I am trying to annotate WGS VCF files through VEP, and even on multi-threading (n=8) the process is painfully slow. The VCF sizes range between 1-1.5Gb. Around 2 days for each VCF What would you recommend to speed up the process? I can break the VCF into chunks. Any other sol. or softwar ...
vcf wgs variant annotation written 4 months ago by Amitm1.6k • updated 4 months ago by Emily_Ensembl17k
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Comment: C: Removing everything after the last underscore in the header of a fastafile
... sorry, I think this is not removing stuff from the last '_' onwards, but just printing the 1st four '_' sep values. ...
written 4 months ago by Amitm1.6k
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Answer: A: Removing everything after the last underscore in the header of a fastafile
... Hi, This should work - awk -F '_' '{if (/^>/) print $1"_"$2"_"$3"_"$4; else print $0;}' test.fasta ...
written 4 months ago by Amitm1.6k
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Answer: C: GISTIC input parameters.
... Hi, Did you provide the 'control' CNV data using the `-cnv` param? That param can be used provide segments that are seen in healthy pop. and/ or control samples. The GISTIC repo. has a file provided for that param, under here - ftp://ftp.broadinstitute.org/pub/GISTIC2.0/hg19_support/ Pick the file ...
written 4 months ago by Amitm1.6k
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Comment: C: Error : run cnvkit from bam
... If it helps, I used the set-up below and it did work fine. cnvkit.py batch \ BAM_files /path/to/tumour/*.bam \ --normal /path/to/germline/*.bam \ --drop-low-coverage \ -p 12 \ --targets my_CNVKit_Targets_AutosomesOnly.bed \ --antitargets my_CNVKit_AntiTargets.bed \ - ...
written 4 months ago by Amitm1.6k
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Comment: C: Error : run cnvkit from bam
... Hi, There seems to be an additional space after the `-r` argument. Can you remove the extra space and run again. Not sure though if this is the main reason, but try ...
written 4 months ago by Amitm1.6k
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Comment: C: Error : run cnvkit from bam
... Hi, If you post the cmd you actually ran, that might be more helpful in finding what might be wrong. ...
written 4 months ago by Amitm1.6k

Latest awards to Amitm

Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Appreciated 5 months ago, created a post with more than 5 votes. For A: Kmer Content in FastQC failed
Scholar 5 months ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Scholar 10 months ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Scholar 12 months ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Appreciated 17 months ago, created a post with more than 5 votes. For A: Kmer Content in FastQC failed
Good Answer 17 months ago, created an answer that was upvoted at least 5 times. For A: Kmer Content in FastQC failed
Popular Question 18 months ago, created a question with more than 1,000 views. For Removing PCR primers in targeted sequencing with nested amplicons
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Scholar 21 months ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Good Answer 22 months ago, created an answer that was upvoted at least 5 times. For A: Kmer Content in FastQC failed
Scholar 2.3 years ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
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Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Commentator 2.5 years ago, created a comment with at least 3 up-votes. For C: Assemble fully overlapping reads into contigs that may have several clones
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Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
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Commentator 2.9 years ago, created a comment with at least 3 up-votes. For C: Assemble fully overlapping reads into contigs that may have several clones
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