User: Duarte Molha

gravatar for Duarte Molha
Duarte Molha230
Reputation:
230
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Location:
Oxford, UK
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Last seen:
1 month, 3 weeks ago
Joined:
8 years, 1 month ago
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Posts by Duarte Molha

<prev • 48 results • page 1 of 5 • next >
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Comment: C: ClinCNV: CNV detection from short reads
... Thanks ... but in relation to the second point I don't think you got the gist of what I was suggesting. I meant saving all the analysis data you do to a given cohort as a data file so that when you rerun and you say you want to only a analyse 1 sample, that initial process of clustering, gender dete ...
written 10 months ago by Duarte Molha230
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Comment: C: ClinCNV: CNV detection from short reads
... thanks could I offer a few suggestions? 1st) on the output tsv file for each sample, for some reason the length_KB field contains spaces. it seems an effort to gae the same number of spaces for each length? I really don't see the point and it will probably just lead to unwanted problems for people ...
written 10 months ago by Duarte Molha230
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Comment: C: ClinCNV: CNV detection from short reads
... the germline... you do not use the TSV files with b-allele frequencies at all? ...
written 10 months ago by Duarte Molha230
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Comment: C: ClinCNV: CNV detection from short reads
... Thanks I am now testing my samples. I am excited to see how your tool performs on them... However I do notice that the threads arguments does not seem to do much to improve speed. I gave it quite a few threads and I can see they are started (in the list of processes running( but they seem to all ...
written 10 months ago by Duarte Molha230
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Comment: C: ClinCNV: CNV detection from short reads
... Thank you for the tool... I am going to test it on a set of my data and I was wondering if you could clarify how you run a set of germline samples against a set of normal germline controls? ...
written 10 months ago by Duarte Molha230
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Comment: C: confused about bcftools roh --ignore-homref option
... as an example... here is my command: > bcftools-1.10.2/bcftools roh -G 30' --AF-dflt 0.4 -I -O region loh.vcf > test_roh > Number of target samples: 1 > Number of --estimate-AF samples: 0 > Number of sites in the buffer/overlap: unlimited > Number of lines total/processed: ...
written 10 months ago by Duarte Molha230
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Comment: C: confused about bcftools roh --ignore-homref option
... Well ... it is of course bialellic ... but it is filtered on BCFtools as non bialellic ... why I am not sure ... that is how they are being reported as filtered ...
written 10 months ago by Duarte Molha230
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confused about bcftools roh --ignore-homref option
... Hi. I am confused about this option on bcftools roh the inclusion of this parameter (--ignore-homref) leads me to the understanding that if I do not include it bcftools orh command, it will consider homozygotic reference SNPS on my input VCF file for ROH calculation. However, as homozygotic refere ...
roh bcftools written 10 months ago by Duarte Molha230
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Comment: C: Why does ExpansionHunter ignore unmapped reads?
... It is a panel capture... but a large panel. I thought of that as well and I have looked at regions where fragileX has some homology... you can get these on the expansion hunter documentation https://github.com/Illumina/ExpansionHunter/blob/master/docs/04_VariantCatalogFiles.md and the coverage th ...
written 12 months ago by Duarte Molha230
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Comment: C: Why does ExpansionHunter ignore unmapped reads?
... I have now looked into the non-mapped reads and you are probably correct... I see no evidence of STR reads unmapped... I am guessing therefore that this is the result of my capture baits unable to capture DNA fragments that are very very GC rich (100% in fact) or realy the bias of the PCR unable to ...
written 12 months ago by Duarte Molha230

Latest awards to Duarte Molha

Popular Question 10 months ago, created a question with more than 1,000 views. For How to visualise RNAseq baits in a genomic context
Popular Question 10 months ago, created a question with more than 1,000 views. For How to I obtain all genotype calls from 1 specific hapmap individual like NA12891
Scholar 11 months ago, created an answer that has been accepted. For A: How To Map Chromosome Coordinates To Ncbi Refseq
Popular Question 2.5 years ago, created a question with more than 1,000 views. For How to visualise RNAseq baits in a genomic context
Epic Question 2.7 years ago, created a question with more than 10,000 views. For How Does Average Heterozygosity Relate To Alellic Frequency Data
Popular Question 3.8 years ago, created a question with more than 1,000 views. For 1000 Genomes Project Community Meeting
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Is It Possible To Filter Only Bookend Reads From A Bed File?
Great Question 4.6 years ago, created a question with more than 5,000 views. For How Does Average Heterozygosity Relate To Alellic Frequency Data
Popular Question 4.6 years ago, created a question with more than 1,000 views. For How Does Average Heterozygosity Relate To Alellic Frequency Data
Popular Question 6.3 years ago, created a question with more than 1,000 views. For How Does Average Heterozygosity Relate To Alellic Frequency Data

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