User: nkausthu

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nkausthu20
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3 years, 5 months ago
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Posts by nkausthu

<prev • 47 results • page 2 of 5 • next >
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Extraction of partially mapped reads from BAM
... Hi, It would be great if anyone can give some suggestion on extracting partially mapped reads from bam/sam generated using BWA or articles which describes more about partially mapped reads. Thank you. ...
partially mapped reads bam bwa written 18 months ago by nkausthu20 • updated 18 months ago by Pierre Lindenbaum126k
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Comment: C: extractPIRs is throwing an ERROR
... Yes .. Programs tells that its duplicate site position but its in different chromosome. But I think it wont be correct if I delete one. ...
written 22 months ago by nkausthu20
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extractPIRs is throwing an ERROR
... I am getting an error while using extractPIRs as follows ./extractPIRs --bam bamlist --vcf VCF.gz --out Reading genotypes in [/MOD_recalibrated_variants.vcf.gz] in VCF format * 477 samples ERROR: Duplicate site pos=52264013 ref=C alt=T How can I avoid this kind of scenario? ...
shapeit extractpirs phasing written 22 months ago by nkausthu20 • updated 22 months ago by genomax78k
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Identification of Common ROH region between two exomes
... Can anyone suggest me the best method to identify common ROH region between two exomes. I have the vcf files for both the samples and I initially used FILTUS but when I cross check FILTUS results manually, I could find heterozygous variants with in the ROH region given by FILTUS. Then I used bcftoo ...
exome roh bcftools filtus written 22 months ago by nkausthu20 • updated 22 months ago by Biostar ♦♦ 20
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Comment: C: Tools for visualization of CNVs called by XHMM
... Thank you so much.. I will explore this and get back to you ...
written 23 months ago by nkausthu20
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Comment: C: Tools for visualization of CNVs called by XHMM
... Please see this link https://ibb.co/dzFKVH ...
written 23 months ago by nkausthu20
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Comment: C: Tools for visualization of CNVs called by XHMM
... Hi, This plot looks like I will be able to get an overview about the deletions and duplication called in each of the sample. Actually I would like to get a plot as below for a specific duplication/deletion. I think it is based on the z-score given by xhmm. ![Duplication][1] [1]: https://ibb.c ...
written 23 months ago by nkausthu20
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Answer: A: Tools for visualization of CNVs called by XHMM
... Thank you so much for the reply. I had tried the XHMM tutorial but an error as follows. ./pseq --group refseq --locdb locdb --group refseq --file /mnt/exome/Softwares/HG19/nexterarapidcapture_exome_target_region.bed --out annotated_targets.refseq ---------------------------------------------------- ...
written 23 months ago by nkausthu20
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Tools for visualization of CNVs called by XHMM
... Hi, I have a list of CNVs called using XHMM from exomes. I would like to know the best way to visualize these CNVs. I hope to get a reply soon. ...
visualization xhmm cnv written 23 months ago by nkausthu20 • updated 23 months ago by bernatgel2.5k
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Answer: A: VisCap 'mat.cov' not found error in R
... I have the same issue. It would be really great if someone can comment on this Attaching package: ‘gplots’ The following object is masked from ‘package:stats’: lowess Attaching package: ‘zoo’ The following objects are masked from ‘package:base’: as.Date, as.Date.numeric character(0) ...
written 23 months ago by nkausthu20

Latest awards to nkausthu

Popular Question 8 months ago, created a question with more than 1,000 views. For Tools for visualization of CNVs called by XHMM
Popular Question 13 months ago, created a question with more than 1,000 views. For Annotation of XHMM VCF file (CNV analysis)
Popular Question 13 months ago, created a question with more than 1,000 views. For Allele frequency calculation
Popular Question 16 months ago, created a question with more than 1,000 views. For Allele frequency calculation
Popular Question 16 months ago, created a question with more than 1,000 views. For Number of homozygous and heterozygous variants

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