User: MAPK

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MAPK1.6k
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Posts by MAPK

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Comment: C: How to set sleep in GNU parallel in a esearch/efetch script
... @genomax I couldn't find anything older than "NCBI_SRA_Metadata_20181202.tar.gz". I need this from 201802. I just created the api_key and exported the variable `export api_key="key"`, but that still won't solve the problem. Where do I add this key? Thank you for your help. ...
written 2 days ago by MAPK1.6k
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How to set sleep in GNU parallel in a esearch/efetch script
... I am requesting NCBI's data and looks like it only allows three requests per second, so I wanted to parallelize requests for three query ids ${IDLIST} per second. I would like to know how I can set sleep time of 2 seconds in this code. I know in a for-loop we can just do `sleep 2`, but what's the sy ...
ncbi sra shell programming written 2 days ago by MAPK1.6k • updated 1 day ago by ole.tange3.8k
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Understanding filters used in plink
... I am new to plink and genotype data and would like to ask about these filters below in plink. I ran this command below to get IBD values, but I am not very clear on `--maf`, `--geno`, ` --allow-no-sex` and `--ld-window-r2` filters. I looked at the explanation on Plink's website, but I am not sure if ...
plink written 10 days ago by MAPK1.6k • updated 10 days ago by h.mon30k
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GATK version differences
... I was wondering if there is a good resource I can check to learn more about what different things have been changed from GATK version to version. I was interested to know the difference specifically between GATK 3.5,36, 4.0, 4.1 and 4.2. Can someone suggest any reference on this? Thanks! ...
gatk written 28 days ago by MAPK1.6k
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Converting Variant ID to RsID in batch
... I have about 200 variant IDs in `chr1:8045045:A:G`, `chr1:8045045:A:G` form. How do I get the corresponding rsIDs(`rs71653621`, `rs71653621`)?. Can someone please point me to the right tool? I am using build 37. ...
rsid snp written 4 weeks ago by MAPK1.6k
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VEP output and protein change
... I have an output file with predicted variant categories from VEP using VCF file. I am confused with the table it generates. For the same SNP, it has different amino acid change (for example, in the picture below, the p change ranges from p.Thr168Ala to p.Thr747Ala). Is there any criteria to choose o ...
vcf vep written 4 weeks ago by MAPK1.6k • updated 4 weeks ago by RamRS28k
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How to combining VEP and VCF in one file
... I was provided a VCF file and a snp-annotated VEP output file separately. I know VEP tool can annotate VCF by adding consequence field of VEP to INFO field of VCF as discussed [here][1]. But is there a way to use VEP output tsv file to annotate VCF INFO column? [1]: https://m.ensembl.org/info/d ...
vcf vep written 5 weeks ago by MAPK1.6k • updated 5 weeks ago by Pierre Lindenbaum129k
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Comment: C: Intersect exome region from whole genome gvcf
... Was it faster? Did you do GenotypeGVCFs afterwards? ...
written 6 weeks ago by MAPK1.6k
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Intersect exome region from whole genome gvcf
... I have been trying to get a joint genotype for exome bed region from whole genome gvcf. However, this is really slow and I am not sure if this is the right approach to do it. I have more than 600 samples and this has been running for more than 10 days. Can someone please clarify? module load ja ...
gatk genomicsdbimport written 6 weeks ago by MAPK1.6k
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Comment: C: Parallel submission of GATK GenomicsDBImport
... It works without parallel. ...
written 6 weeks ago by MAPK1.6k

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Student 5 days ago, asked a question with at least 3 up-votes. For R programming, concatenate or combine all the column contents
Popular Question 14 days ago, created a question with more than 1,000 views. For Complete Genomics data analysis, pipeline version and batch effect
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Great Question 5 months ago, created a question with more than 5,000 views. For What are the terms for reference allele and alternate alleles in cancer?
Popular Question 5 months ago, created a question with more than 1,000 views. For Reverse translate and get the genomic position
Great Question 5 months ago, created a question with more than 5,000 views. For R programming, concatenate or combine all the column contents
Popular Question 5 months ago, created a question with more than 1,000 views. For Complete Genomics data analysis, pipeline version and batch effect
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