User: QVINTVS_FABIVS_MAXIMVS

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There's more than one way to hunt a CNV

Posts by QVINTVS_FABIVS_MAXIMVS

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Mouse Strains in mm10/GRCm38 dbSNP 142?
... 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 ...
mm10 hisat2 dbsnp mouse written 12 days ago by QVINTVS_FABIVS_MAXIMVS2.3k • updated 12 days ago by igor9.2k
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Comment: C: Missing MQ tag from bwa mem alignments
... I was referring to SAM/BAM file MQ tag. Unfortunately sometimes I have to use legacy code. ...
written 4 weeks ago by QVINTVS_FABIVS_MAXIMVS2.3k
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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 4 weeks ago by QVINTVS_FABIVS_MAXIMVS2.3k
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Missing MQ tag from bwa mem alignments
... 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 ...
wgs mem alignment bwa written 4 weeks ago by QVINTVS_FABIVS_MAXIMVS2.3k • updated 4 weeks ago by benformatics1.3k
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BQSR BD/BI Tags into integer values?
... 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! ...
gatk bqsr written 4 weeks ago by QVINTVS_FABIVS_MAXIMVS2.3k
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Answer: A: Is GRCh37 and hg19 are the same?
... 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 4 weeks ago by QVINTVS_FABIVS_MAXIMVS2.3k
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BED to HDF5 in Python. Simple Script?
... 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 ...
python hdf5 bed written 3 months ago by QVINTVS_FABIVS_MAXIMVS2.3k
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Alternatives to CNVnator?
... 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 ...
copy number variation cnv written 3 months ago by QVINTVS_FABIVS_MAXIMVS2.3k • updated 3 months ago by jared.andrews074.3k
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Samtools view -f "OR" operator possible?
... 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 ...
samtools written 6 months ago by QVINTVS_FABIVS_MAXIMVS2.3k • updated 6 months ago by dariober10k
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Comment: C: BWA MEM Definition of a Primary Alignment
... Thanks for not answering my question. For chimeric reads (i.e for this example true split-reads that for SV informative) the difference between secondary and supplementary is semantic, a secondary alignment would map to another position but be clipped in a manner that is supporting a breakpoint. Som ...
written 7 months ago by QVINTVS_FABIVS_MAXIMVS2.3k

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