User: rightmirem

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rightmirem50
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Posts by rightmirem

<prev • 27 results • page 1 of 3 • next >
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Using synonymous vs. non-synonymous ALT for SNP data validation
... I'm looking again at validating SNP calls (whole genome) and stumbled across this article [The effect of strand bias in Illumina short-read sequencing data][1] ...in which the author(s) mention ... > ...the number of novel non-synonymous SNPs can also be a very good indicator of the false posi ...
alignment next-gen snp sequencing written 11 months ago by rightmirem50
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Comment: C: bcftools filter by ALT == '.'
... Worked brilliantly. Thanks! ...
written 11 months ago by rightmirem50
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bcftools filter by ALT == '.'
... I have a large vcf.gz file for 70 samples. It contains many positions where all 70 samples match the reference. I'd like to filter those lines out. I tried: bcftools filter -e '%ALT == .' ./SIDXXX.vcf.gz but it came back with ... [filter.c:1741 filters_init1] Error: the tag "INFO/%ALT" ...
next-gen sequence snp sequencing written 11 months ago by rightmirem50 • updated 11 months ago by Pierre Lindenbaum115k
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HiSAT2 segfault after long run
... I was running ```hisat2-build``` against a very large, multiple sample VCF file. After almost 3 days of running, it finally ***segfault*** 'ed... hisat2-build --large-index -p40 --snp /(snip)/SIDXXX-A.merged.snp --haplotype /(snip)/SIDXXX-A.merged.haplotype /(snip)/GRCh38_87.fa /(snip)/SIDXXX ...
assembly next-gen snp alignment written 12 months ago by rightmirem50 • updated 12 months ago by Kevin Blighe33k
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Answer: A: Passing VCF file directly into ```HiSAT2-build --snp --haplotype```
... So, found my own answer. I'll leave this here in case the question comes up again. The ```--snp```switch must be used (only) with the hisat2 format (as described above). It **WILL** actually run and produce output if you feed in a VCF file directly - but my understanding is this is purely accident ...
written 12 months ago by rightmirem50
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Passing VCF file directly into ```HiSAT2-build --snp --haplotype```
... We've been working with ```HiSAT2```and ```HiSAT2-build``` for mapping NGS data to a reference. In the next step, we wish to create a new indexed reference from VCF data we've generated. My PI says to use... hisat2-build --snp ./MySNPs.vcf.gz --haplotype Grch38.fa OutfilesIndexed ... to ...
next-gen alignment snp hisat2 written 12 months ago by rightmirem50
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Comment: C: Recreating a Genomic reference (.fastq) from a BCF file
... Or maybe you mean I need a fastA, not a fastQ? ...
written 12 months ago by rightmirem50
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Comment: C: Recreating a Genomic reference (.fastq) from a BCF file
... Thanks! I'm not sure what you mean when you say "fastq is not a reference-thing". I realize fastq is not "specifically" just for reference genomes. But I assume that it's the best file choice *for* a reference genome...in the sense that the original reference I used was a fastq run through HiSAT2 ...
written 12 months ago by rightmirem50
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Recreating a Genomic reference (.fastq) from a BCF file
... I'm asking here before I go off half-cocked and try to build my own solution. Simply put, I have been using the **reference GRCh38**, created **BAM** files via ```HiSAT2```, and then **BCF** files using ```samtools mpileup | bcftools call | bcftools norm```. The BCF tools include the REF/REF mat ...
assembly next-gen snp alignment written 12 months ago by rightmirem50
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Comment: C: Under what circumstances does "REF | REF" (or REF / REF) show up in the VCF/BCF
... "BCFTools could easily call 0/0 genotypes, but why would it?" Well, exactly my thought actually :D All my BCF files have "./.:." for samples that are REF/REF. But this one had "0|0" meaning it's not a variant, but a reference. So I couldn't figure out why they were there :D ...
written 13 months ago by rightmirem50

Latest awards to rightmirem

Scholar 12 months ago, created an answer that has been accepted. For A: Passing VCF file directly into ```HiSAT2-build --snp --haplotype```
Supporter 12 months ago, voted at least 25 times.

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