User: QVINTVS_FABIVS_MAXIMVS

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Posts by QVINTVS_FABIVS_MAXIMVS

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Comment: C: bedtools coverage bed
... One "hack" (I hesitate to call it a solution) is to use `samtools depth`. This command will print out the number of reads spanning a nucleotide for a genome or a given region (`samtools depth in.bam -r chr1:1-1000000`). However, `samtools depth` does not give you the same output as `coverageBed`, b ...
written 6 days ago by QVINTVS_FABIVS_MAXIMVS2.0k
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Comment: C: bcftools merge failed: incorrect number of PL fields
... Ahh I see. Thanks for the help ...
written 6 days ago by QVINTVS_FABIVS_MAXIMVS2.0k
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Comment: C: bcftools merge failed: incorrect number of PL fields
... Thanks, I've used `bcftools norm` to left-align and to split multiallelic sites into biallelic sites (for plink). I solved the issue by removing the PL entries. How would `bcftools norm` work in this situation of differing versions? ...
written 6 days ago by QVINTVS_FABIVS_MAXIMVS2.0k
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bcftools merge failed: incorrect number of PL fields
... I'm using `bcftools merge` and I get this error ``` Incorrect number of PL fields (3) at chr1:10240, cannot merge. ``` I believe this is due to different versions of bcftools/GATK. However, I do not care about the PL fields. Is there a way for me to skip this error (make it a warning) or do I have ...
vcf merge bcftools written 7 days ago by QVINTVS_FABIVS_MAXIMVS2.0k
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Answer: A: Mutation analysis on RNAseq
... `chr1 13684 C T 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0` Looks like a formatting error as swbarnes2 commented. VCF files are formatted as such CHROM PO ...
written 28 days ago by QVINTVS_FABIVS_MAXIMVS2.0k
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Comment: C: How to determine parent of origin of phased variants when all members are het
... Lame. I was afraid this was the case. The phasing leveraged nanopore long reads, so the blocks are really long. You would think that phasing software that uses inheritance information would encode the parent of origin. Thanks for the insight. To add, if anyone knows of a software that can assign par ...
written 28 days ago by QVINTVS_FABIVS_MAXIMVS2.0k
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How to determine parent of origin of phased variants when all members are het
... I'm a little confused on the format of phased variants in a VCF file. I was under the assumption that `A|B` is equal to `Paternal Haplotype | Maternal Haplotype` but I believe it's `Haplotype Block A | Haplotype Block B`. So in the case of KID DAD MOM 0|1 0|1 0|1 How do ...
vcf phase written 28 days ago by QVINTVS_FABIVS_MAXIMVS2.0k • updated 28 days ago by WouterDeCoster24k
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UCSC Roadmap Epigenomics Hub: "Summary" tracks
... I'm using data from the Roadmap Epigenomics Data Complete Collection at Wash U VizHub Hub on UCSC. Using the table browser, I noticed there are "Summary" tracks along with the "regular" tracks. I can't find the appropriate documentation. But what's the difference between the two? ![Example][1] ...
roadmap ucsc written 4 weeks ago by QVINTVS_FABIVS_MAXIMVS2.0k
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Comment: C: RefSeq Transcript without a 5'UTR?
... Thank you for pointing that out. Makes perfect sense. ...
written 6 weeks ago by QVINTVS_FABIVS_MAXIMVS2.0k
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RefSeq Transcript without a 5'UTR?
... I'm defining exon and intron positions using the RefSeq table from UCSC. The raw table is formatted as such ---------- CHROM Strand Transcription-Start Transcription-End Coding-Start Coding-End .... I've noticed for this transcript (hg38 RefSeq) NM_001304569.1 the transcriptio ...
refseq written 6 weeks ago by QVINTVS_FABIVS_MAXIMVS2.0k

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