User: aiteteji

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aiteteji10
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Posts by aiteteji

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Comment: C: Analogy of exifread library in pysam for bam and vcf header files
... Thanks for posting the link. I read it, but I didn't get how to remove the "@" in .bam and "##" in vcf file. I was hoping that someone who knows better can help. Here is my approach: import pysam pysamlist = [] with pysam.AlignmentFile("ex1.bam", "rb") as f: tags = pysam. ...
written 7 months ago by aiteteji10 • updated 7 months ago by finswimmer12k
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Analogy of exifread library in pysam for bam and vcf header files
... Hi Biostars community, Is there an analogous way in Pysam to the code below to extract the header information in .bam and .vcf (or .vcf.gz) files? Help with a code snippet will great. The code snippet below uses exifread library to get the meta-info (in key-value pair) in jpeg and tiff files. imp ...
vcf bam bcftools pysam htslib written 7 months ago by aiteteji10
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Get Rs Number Based On Chromosome and Position
... Hello Biostars, I have a list of chromosome and coordinates in my vcf file, see examples: 1:10327 1:10434 1:10440 1:10469 ... Is there anyway to get the rs number for each coordinate using plink or bcftools? I found some old answers here, but I'll like to know how this is curr ...
vcf rna-seq snp written 10 months ago by aiteteji10 • updated 10 months ago by Emily_Ensembl19k
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Extract metadata from .ped and .map file
... I want to archive some .ped and associated .map files. But do not know if any, how to extract the embedded metadata in them. These metadata are expected to aid data discovery that helps in the querying of the database to find matching objects. Anyone has idea if there are standards to use to curate ...
.map plink .ped metadata written 13 months ago by aiteteji10

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