User: amitgourav.ghosh12

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Posts by amitgourav.ghosh12

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Comment: C: Segmentation fault error while running extractPIRs from ShapeIT
... No worries! Thank you very much for your help. Sincerely, Amit ...
written 8 months ago by amitgourav.ghosh1260
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Comment: C: Segmentation fault error while running extractPIRs from ShapeIT
... Hello! Did you find the reason behind the segmentation fault error? Mine comes without the core dumped statement. It looks like this: /var/spool/pbs/mom_priv/jobs/8948248.wlm01.SC: line 35: 3365 Segmentation fault Sincerely, Amit ...
written 8 months ago by amitgourav.ghosh1260
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SNPduo error reading ped files
... Hello, I tried submitting my map and ped files for IBS and relationship calculation between samples in SNPduo. It was able to read the map file but it gave an error when it tried to read the ped file. The error looks like this: ****Reading Ped file [ /..path/filename.ped ]** **[Error] No ...
genome snpduo ibs ped file written 9 months ago by amitgourav.ghosh1260 • updated 9 months ago by RamRS27k
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Comment: C: Replace missing SNPs of one individual with reference alleles in a VCF file
... The reason to do so because of that sample being an ancient individual had many missing genotypes, thereby messing up my final pca output. ...
written 11 months ago by amitgourav.ghosh1260
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Comment: C: Replace missing SNPs of one individual with reference alleles in a VCF file
... Good question, I am not so sure. Let me find out how the PCA comes out. Meanwhile, I have figured out a possible way to do it. I converted my ld-pruned bed, bim and fam file to vcf file in plink. It only has the genotypes without the quality parameters. Probably it would be much easier to conver ...
written 12 months ago by amitgourav.ghosh1260
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Replace missing SNPs of one individual with reference alleles in a VCF file
... Hello, I have a vcf file of about 565 individuals. I want to replace the missing SNPs of one of them (Ancient sample) with the reference alleles. I was thinking about trying out the following- $ bcftools +fixploidy phasedVCF-short02.vcf.gz -- -f 2|bcftools +missing2ref - -- -p > phasedVCF ...
bcftools vcftools snp sequencing written 12 months ago by amitgourav.ghosh1260 • updated 12 months ago by zx87549.2k
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Change rsID to chromosome:location in bim files for plink
... Some of the SNPs in my dataset are without rs ids, so in the bim file, they have dots instead of rs ids for them. So for errorless analysis how should replace the rs id column with that of the chromosome: location column instead? ...
genome plink snp written 12 months ago by amitgourav.ghosh1260 • updated 12 months ago by chrchang5236.9k
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Comment: C: VCFtools: --window-pi and --from-bp --to-bp produces different start and ending
... Hello Sir, I am facing the same problem. I somewhat managed to get one whole region to come as one in Tajima's D calculation but I am unable to do so for the pi calculation. Did you find a way to overcome this problem? I yes, can you please suggest me what to do? Thanking you, Amit ...
written 2.0 years ago by amitgourav.ghosh1260
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Comment: C: Tajima's D Using SNP data ONLY
... Even I also have SNP data, can you please suggest how to compute Tajima's D without vcf files? Thank you! ...
written 2.1 years ago by amitgourav.ghosh1260
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Comment: C: How to do Tajima's D analysis?
... Hello Sir, indeed there are plenty of questions in the site. What I learnt till now is that one can use the package "pegas" in R or use dnasp v.5 or vcf tools for this purpose. I have binary format files from plink and the individuals respective MAFs, but not sequences. I am planning to download vcf ...
written 2.1 years ago by amitgourav.ghosh1260

Latest awards to amitgourav.ghosh12

Popular Question 4 months ago, created a question with more than 1,000 views. For Removing SNPs with over 2% missing rate in plink
Popular Question 7 months ago, created a question with more than 1,000 views. For Use plink to extract data using common SNPs and merge this into one file
Popular Question 12 months ago, created a question with more than 1,000 views. For Removing SNPs with over 2% missing rate in plink
Supporter 12 months ago, voted at least 25 times.
Popular Question 14 months ago, created a question with more than 1,000 views. For Removing SNPs with over 2% missing rate in plink
Popular Question 23 months ago, created a question with more than 1,000 views. For How to do pca plot from .eigenval and .eigenvec files from Plink in R.

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