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 10 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 10 months ago by Amitm1.6k
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Comment: C: faster variant annotation for large VCFs
... many thanks! Going to try this ...
written 10 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 10 months ago by Amitm1.6k • updated 10 months ago by Emily_Ensembl18k
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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 10 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 10 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 10 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 10 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 10 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 10 months ago by Amitm1.6k

Latest awards to Amitm

Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Appreciated 11 months ago, created a post with more than 5 votes. For A: Kmer Content in FastQC failed
Scholar 11 months ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Scholar 16 months ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Scholar 18 months ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Appreciated 23 months ago, created a post with more than 5 votes. For A: Kmer Content in FastQC failed
Good Answer 23 months ago, created an answer that was upvoted at least 5 times. For A: Kmer Content in FastQC failed
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Removing PCR primers in targeted sequencing with nested amplicons
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Scholar 2.2 years ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Good Answer 2.4 years ago, created an answer that was upvoted at least 5 times. For A: Kmer Content in FastQC failed
Scholar 2.8 years ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Scholar 2.9 years ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Appreciated 2.9 years ago, created a post with more than 5 votes. For A: Kmer Content in FastQC failed
Guru 2.9 years ago, received more than 100 upvotes.
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Commentator 3.0 years ago, created a comment with at least 3 up-votes. For C: Assemble fully overlapping reads into contigs that may have several clones
Voter 3.2 years ago, voted more than 100 times.
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
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Commentator 3.4 years ago, created a comment with at least 3 up-votes. For C: Assemble fully overlapping reads into contigs that may have several clones
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA

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