User: QVINTVS_FABIVS_MAXIMVS
QVINTVS_FABIVS_MAXIMVS • 2.4k
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There's more than one way to hunt a CNV
Posts by QVINTVS_FABIVS_MAXIMVS
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... In the past, my 40x WGS BAMs take about 2-6 hours to run sambamba markdups with 12-24 threads. I have received a batch of BAMs that are taking over 7 days to run. The file size is the same, and so is the sequencing center.
Any ideas what could cause this step to take much longer than expected? ...
written 4 months ago by
QVINTVS_FABIVS_MAXIMVS • 2.4k
• updated
10 weeks ago by
Biostar ♦♦ 20
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... I am using the pre-built HiSat2 index for mm10 with the snps. Looking at the script the devs provide, I can see they are using SNPs from UCSC golden path. https://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/snp142Common.txt.gz
However, I would like to know which strains are included for this r ...
written 5 months ago by
QVINTVS_FABIVS_MAXIMVS • 2.4k
• updated
5 months ago by
igor ♦ 11k
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... I was referring to SAM/BAM file MQ tag. Unfortunately sometimes I have to use legacy code. ...
written 6 months ago by
QVINTVS_FABIVS_MAXIMVS • 2.4k
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Answer:
A: lumpy for cnv detection
... You should merge the SVs and genotype them. Hopefully your plant is diploid since svtyper is for diploid organisms. Perhaps, it can handle higher ploidies.
I would follow the methods outlined in this paper https://www.nature.com/articles/s41467-018-06159-4
The developers of lumpy/svtyper contribu ...
written 6 months ago by
QVINTVS_FABIVS_MAXIMVS • 2.4k
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... I am using BWA MEM 0.7.17 for all my paired-end alignments.
Can someone clue me in on why some alignments have a `MQ` tag and others do not?
The commands are identical in some cases. Does BQSR apply this tag, there could be a difference in the options at this step perhaps? And I think some align ...
written 6 months ago by
QVINTVS_FABIVS_MAXIMVS • 2.4k
• updated
6 months ago by
benformatics • 1.6k
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... I want to convert the values in the BI and BD tags into integer values. However, I cannot find any documentation online that has the conversion table.
If someone knows where I can find this, please link me to it!
...
written 6 months ago by
QVINTVS_FABIVS_MAXIMVS • 2.4k
• updated
5 months ago by
Biostar ♦♦ 20
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... GRCh37d5 is different since there is a decoy sequence that may not be present in some hg19 builds. Also if memory serves me GRCh37 with or without decoy hard masks the pseudoautosomal regions on chrY, therefore you treat the pseudoautosomal region on chrX as diploid in males. I do not think some of ...
written 6 months ago by
QVINTVS_FABIVS_MAXIMVS • 2.4k
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... I'm looking for some simple boilerplate script that efficiently converts a BED file (only Chrom Start End) to HDF5 in python.
All the examples I see online are convoluted and bloated with functions that I do not need (HI-C/GTF).
I do not need a CLI script, I would like to implement a BED -> H ...
written 8 months ago by
QVINTVS_FABIVS_MAXIMVS • 2.4k
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... I think I have put over 36 man hours in trying to get CNVnator to install. I have tried nearly every avenue, conda, environments, etc... and still cannot get it to install.
I am at my wits end, what are comparable CNV calling algorithms for whole genomes that use read depth. Basically I'm looking ...
written 9 months ago by
QVINTVS_FABIVS_MAXIMVS • 2.4k
• updated
3 months ago by
astulaaa • 0
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... Quick question:
Is it possible to do a `samtools view -f XXX` using a `OR` operator?
Say if I wanted to get all reads that were unmapped (`4`) or supplementary alignments (`2048`).
Is this possible? Because doing a `2052` is an "AND" (reads are unmapped and supplementary alignments which is imp ...
written 12 months ago by
QVINTVS_FABIVS_MAXIMVS • 2.4k
• updated
12 months ago by
dariober ♦ 11k
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