User: Ishtiaq Ahmad Khan

Reputation:
50
Status:
Trusted
Location:
Pakistan
Website:
https://www.iccs.edu/
Last seen:
1 year, 1 month ago
Joined:
3 years, 11 months ago
Email:
i*************@gmail.com

Posts by Ishtiaq Ahmad Khan

<prev • 19 results • page 1 of 2 • next >
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Conversion of VCF file to Vranges
... I am using SomaticSignature Package for analysis of TCGA data. I have VCF file and need to convert it in vranges. How can I do this conversion. ...
R written 3.2 years ago by Ishtiaq Ahmad Khan50 • updated 3.1 years ago by spaladug10
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EIGENSOFT INSTALLATION ISSUES
... LAPACK is required for proper functioning of EIGENSOFT. I am trying to install LAPACK and it is ending up with following error gfortran: error: ../../librefblas.a: No such file or directory make[1]: *** [../xblat1s] Error 1 make[1]: Leaving directory `/home/linux/Working/software/eigensoft-master/l ...
software error written 3.3 years ago by Ishtiaq Ahmad Khan50
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Comment: C: Drawing Chromosome Ideograms With Data
... How to add X and Y chromosomes in the above ideogram.  ...
written 3.6 years ago by Ishtiaq Ahmad Khan50
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Comment: C: Convert plink files to VCF: Reference allele file
... It worked really fine. Thanks Philipp! ...
written 3.8 years ago by Ishtiaq Ahmad Khan50
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Convert plink files to VCF: Reference allele file
... I am trying to convert plink files to VCF by using following commands  #!/bin/sh # 1. have plink binary to specify reference allele plink --noweb --bfile $plink_file --reference-allele $ref_Allele_file --make-bed --out $plink_file_modified # 2. create plinkseq project pseq $pseq_project new-projec ...
genome snp written 3.8 years ago by Ishtiaq Ahmad Khan50 • updated 2.7 years ago by willgilks260
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Answer: A: Annovar and CADD Annotation
...  Here is a comparison of CADD scores (build 19) for different versions. Why it is so different some time??  CHROM# Position  REF Alt V1.0 V1.1 V1.2 V1.3  1 12854074 C A 14.29 23 22.4 23.5 1 17301446 G C 14.3 21.6 ...
written 3.8 years ago by Ishtiaq Ahmad Khan50
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Annovar and CADD Annotation
... I CADD scored my set of variants called on build 38 by using Annovar. Then I converted my coordinates to hg19 by crossmap and liftover separately and scored them using CADD database and script. The output is quite different. I double checked my coordinate conversion and it is fine. But CADD server a ...
snp written 3.8 years ago by Ishtiaq Ahmad Khan50 • updated 3.8 years ago by Vivek2.2k
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Processing multi sample VCF file
... I have a multi sample VCF and want to run folloing command to extract novel SNPs bcftools view -s  sample -n singleton.1_22_XY.snp144.vcf.gz I want to run this command one by one on all samples in multisample VCF to get separate out put.  ...
snp written 3.9 years ago by Ishtiaq Ahmad Khan50
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Comment: C: Extracting Novel SNPs from VEP output
... Many Thanks  ...
written 3.9 years ago by Ishtiaq Ahmad Khan50
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Extracting Novel SNPs from VEP output
... I run command based VEP for annotation. I want to extract only NOVEL SNPSs according to rs ID in first coulmn. How I can do this.  1_17538_C/T     1:17538 T       ENSG00000278267 ENST00000619216 Transcript      upstream_gene_variant   -        1_17538_C/T     1:17538 T       ENSG00000223972 ENST000 ...
snp written 3.9 years ago by Ishtiaq Ahmad Khan50

Latest awards to Ishtiaq Ahmad Khan

Epic Question 18 months ago, created a question with more than 10,000 views. For Convert plink files to VCF: Reference allele file
Popular Question 18 months ago, created a question with more than 1,000 views. For Annovar and CADD Annotation
Popular Question 18 months ago, created a question with more than 1,000 views. For Processing multi sample VCF file
Popular Question 18 months ago, created a question with more than 1,000 views. For Statistical Analysis of VCF
Popular Question 18 months ago, created a question with more than 1,000 views. For dbSNP 144 for Annovar
Great Question 2.5 years ago, created a question with more than 5,000 views. For Convert plink files to VCF: Reference allele file
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Annovar and CADD Annotation
Popular Question 2.5 years ago, created a question with more than 1,000 views. For dbSNP 144 for Annovar
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Convert BED(UCSC) to VCF
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Convert plink files to VCF: Reference allele file

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