User: dmyersturnbull

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90
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New User
Location:
Stanford University
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3 years, 9 months ago
Joined:
4 years, 6 months ago
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Posts by dmyersturnbull

<prev • 10 results • page 1 of 1 • next >
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VQSR on non-variant positions
... We have a set of whole-genome Illumina DNA sequences. We're using GATK HaplotypeCaller followed by VQSR, both of which the GATK recommends. We're interested in only a set of positions that are known to (commonly) contain SNPs, all of which are in dbSNP. For this, we want a list of genotype calls, o ...
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Comment: C: HaplotypeCaller with --dbsnp does not populate ID column
... Thanks. That's concerning, then. I thought VCF was always 1-based. However, I don't think that's the issue, since, with BP_RESOLUTION, literally every position is called (chr1:1, chr1:2, chr1:3, ...). ...
written 4.4 years ago by dmyersturnbull90
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HaplotypeCaller with --dbsnp does not populate ID column
... I want to obtain a VCF file containing genotype calls and their scores for every rsID, whether or not a variant was called. I was planning to use the following steps: HaplotypeCaller -genotyping_mode DISCOVERY --output_mode EMIT_VARIANTS_ONLY  --emitRefConfidence BP_RESOLUTION as shown above awk ...
haplotypecaller gatk next-gen variant calling written 4.4 years ago by dmyersturnbull90 • updated 4.4 years ago by Jordan1.1k
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Comment: C: GRCh38 BAM with hg38 VCFs
... Thanks! I'm glad that the masking isn't an issue. For the second concern, I am using no_alts, but the readme mentions it includes an Epstein-Barr viral sequence as a decoy as well as unplaced and unlocalized scaffolds (aside: what's the difference between unplaced and unlocalized?). My understandin ...
written 4.4 years ago by dmyersturnbull90
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Comment: C: GRCh38 BAM with hg38 VCFs
... Thanks. The sequences for GRCh38 and hg38 are nearly identical. However, hg38 seems to have more 'N's and 'n's, at least. Second, the GRCh38 "analysis set" contains coordinates that hg38 (and GRCh38) doesn't. Third, the headers differ wildly: GRCh38: >gi|568336022|gb|CM000664.2| Homo sapiens ch ...
written 4.4 years ago by dmyersturnbull90
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Representative set for normal structural variation
... I'm simulating variation in a human genome, but I want to restrict simulated structural variants to places where they're known to occur. For this, I'm interested in assessing which parts of the human genome (introns, exons, and intergenic regions) are, in an average human, more, or less, structurall ...
genome structural variants svs dbvar dgv written 4.4 years ago by dmyersturnbull90
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GRCh38 BAM with hg38 VCFs
... I have a BAM file containing an alignment to the GRCh38 "analysis pipeline" set with decoys (from ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh38/ seqs_for_alignment_pipelines/). I remapped NCBI's "resource bundle" VCF files to UCSC's hg38 using a combination ...
genome next-gen written 4.5 years ago by dmyersturnbull90 • updated 4.4 years ago by Denise - Open Targets4.8k
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Answer: A: Undo alignment using bamtofastq, after dedup
... Thanks—that answers my question. For anyone else interested in this question, the Broad Institute has a guide: http://gatkforums.broadinstitute.org/discussion/2908/howto-revert-a-bam-file-to-fastq-format ...
written 4.5 years ago by dmyersturnbull90
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Comment: C: Undo alignment using bamtofastq, after dedup
... Thanks! I updated my post. ...
written 4.5 years ago by dmyersturnbull90
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Undo alignment using bamtofastq, after dedup
... I'm a newcomer to the sequencing world. From another lab, I have a large (full human genome) mate-pair BAM file produced from the following steps: 1. Trimming of reads to 30bp for PHRED scores under 20 (software unknown). 2. Alignment against GRCh37 with BWA 0.5.8a. 3. De-duplication with GATK 1. ...
genome next-gen written 4.5 years ago by dmyersturnbull90

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Popular Question 3.8 years ago, created a question with more than 1,000 views. For GRCh38 BAM with hg38 VCFs

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