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User: bioinfo89

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bioinfo89 • 10
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Posts by bioinfo89

<prev • 42 results • page 1 of 5 • next >
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Comment: C: How to filter variant calls based on specific reference and alternate allele fre
... Hi Nandini, Could you suggest what parameter to take using select variants which would help to achieve what I want? Thanks! ...
written 28 days ago by bioinfo89 • 10
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Comment: C: How to filter variant calls based on specific reference and alternate allele fre
... I have one vcf per sample! Thanks I will try this! ...
written 29 days ago by bioinfo89 • 10
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How to filter variant calls based on specific reference and alternate allele frequency ratio during variations calling?
... Hi All, I have been working on targeted amplicon sequencing data (>200 samples). I use GATK for variant calling. So my question is, is there a parameter in variant calling where we can specify to not call variants if the reference allele frequency is say >0.8 than the alternate allele frequen ...
vcf snp written 29 days ago by bioinfo89 • 10 • updated 29 days ago by finswimmer ♦ 3.6k
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Comment: C: How to extract the coordinates for the BRCT domain (BRCA1) nucleotide sequence?
... I used it to get the result. But the mapped regions were scattered. (eg. 1 to 63 of the query mapped to different coordinate, 64 to 123 mapped to different coordinate etc). ...
written 6 weeks ago by bioinfo89 • 10
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Comment: C: How to extract the coordinates for the BRCT domain (BRCA1) nucleotide sequence?
... Blastn from Ensembl! ...
written 6 weeks ago by bioinfo89 • 10
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Comment: C: How to extract the coordinates for the BRCT domain (BRCA1) nucleotide sequence?
... No it gives the corresponding nucleotide sequence (known Genbank accession ID). ...
written 6 weeks ago by bioinfo89 • 10
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How to extract the coordinates for the BRCT domain (BRCA1) nucleotide sequence?
... Hi all, I am working on breast cancer data. I have protein sequence for BRCT domain and I want know its nucleotide sequence coordinates. I tried using tblastn to get the corresponding nucleotide sequence (~294bp) and then I used ensemble blast to get the coordinates of the nucleotide sequence obtai ...
sequence written 6 weeks ago by bioinfo89 • 10
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How to extract ampliconID from a bed file of each called variant from a vcf?
... Hi All, I want to extract ampliconIDs for all the variants called in multiple samples. I have VCFs for each sample (~200) and I have a bed file with chrno,amplicon start and end coordinates and ampliconIDs. So for each variant, I want to extract the corresponding ampliconID in which it falls based ...
next-gen snp written 10 weeks ago by bioinfo89 • 10 • updated 10 weeks ago by finswimmer ♦ 3.6k
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Comment: A: How to extract unique paired end reads from a merged BAM file?
... You can check this link:https://github.com/alvaralmstedt/Tutorials/wiki/Separating-mapped-and-unmapped-reads-from-libraries ...
written 10 weeks ago by bioinfo89 • 10
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Answer: A: How to extract unique paired end reads from a merged BAM file?
... A found a simple solution! Used `seqtk subseq` extract all the unique unmapped reads! ...
written 11 weeks ago by bioinfo89 • 10 • updated 4 weeks ago by Vijay Lakhujani ♦ 2.8k

Latest awards to bioinfo89

Scholar 11 weeks ago, created an answer that has been accepted. For A: How to extract unique paired end reads from a merged BAM file?
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