User: SOHAIL

gravatar for SOHAIL
SOHAIL190
Reputation:
190
Status:
Trusted
Location:
Beijing Institute of Genomics, CAS.
Last seen:
1 month, 3 weeks ago
Joined:
2 years, 11 months ago
Email:
m*****************@live.com

Posts by SOHAIL

<prev • 57 results • page 1 of 6 • next >
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Calculate the genotype frequency
... Hi everyone: I have a VCF file having multiple population samples. Is there any way to calculate the observed counts of genotypes called and observed genotype frequency of a subset of individuals from a given population within VCF file? For example (genotype freq) : 0|0 : 0.2, 0|1: 0.5, 1|1: 0 ...
vcf ngs written 8 weeks ago by SOHAIL190 • updated 8 weeks ago by Wietje150
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Answer: A: flagstats results show 0.0 % properly paired reads
... @joshuau490 Hi, Please find the answer in my posted thread at: https://gatkforums.broadinstitute.org/gatk/discussion/5786/gatk-flagstats-show-0-0-properly-paired-reads hope it helps. -sohail ...
written 3 months ago by SOHAIL190
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Comment: C: calculate Per variant Heterozygosity from VCF file
... It worked perfectly fine.. thanks for the help.. @Kevin ...
written 5 months ago by SOHAIL190
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calculate Per variant Heterozygosity from VCF file
... Hi everybody, Is there any way to calculate the per variant heterozygosity (i.e. number of 1/0 or 0/1 genotypes observed at given variant site for set of individuals in VCF file) from VCF file? I knew per individual heterozygosity can be calculated by --het tag from VCFtools Thanks! -sohail ...
vcf ngs written 5 months ago by SOHAIL190 • updated 5 months ago by Kevin Blighe21k
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tools for Population branch statistics (PBS)
... Hi, Can anyone please suggest a tool/script for calculating Population Branch statistics (PBS) test scores for large number of variant sites from NGS data set (i.e. VCF files)? Regards sohail ...
ngs selection scans written 9 months ago by SOHAIL190 • updated 4 months ago by GabrielMontenegro400
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Comment: C: Switch the position of REF/ALT alleles based on AA (ancestral allele) annotation
... Problem solved...! Thanks ...
written 10 months ago by SOHAIL190
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Comment: C: Switch the position of REF/ALT alleles based on AA (ancestral allele) annotation
... Hi @Pierre, Thank you for suggesting your useful scripts as always. :).. however, i have some problems in vcffilterjdk installation. i have posted the issue [here][1] Please have look. [1]: https://github.com/lindenb/jvarkit/issues/82 ...
written 10 months ago by SOHAIL190
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Comment: C: Switch the position of REF/ALT alleles based on AA (ancestral allele) annotation
... Hi @Pierre I have shared the Sample VCF file (header + few variants with possible conditions) Please have a look (two files). [Sample.vcf at gist][1] [1]: https://gist.github.com/muhammadsohailraza/3b371464c95c2ffde353f59879df6742 ...
written 10 months ago by SOHAIL190
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Switch the position of REF/ALT alleles based on AA (ancestral allele) annotations in VCF
... Hi! I have a VCF file with AA annotations from EPO. I want to switch the REF/ALT position of the REF/ALT alleles along with the respective genotypes of individuals accordingly, For instance, I have one VCF record such as 1 936210 rs3121569 C A 124552 PASS AC=236;AF ...
vcf ngs written 10 months ago by SOHAIL190 • updated 8 weeks ago by dkmanruiz0
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PSMC analysis: input data processing, mutation rate, generation time
... Hi Everybody, I have few questions regarding PSMC analysis, can anyone please guide me.. 1. What are the general masking filters that would be applied during input files processing in PSMC analysis for reliable results, and how to apply them? 2. During plotting PSMC plot construction, how to deci ...
psmc written 15 months ago by SOHAIL190

Latest awards to SOHAIL

Popular Question 3 months ago, created a question with more than 1,000 views. For Processing FASTQ files after fastq-dump
Popular Question 3 months ago, created a question with more than 1,000 views. For Processing FASTQ files after fastq-dump
Popular Question 5 months ago, created a question with more than 1,000 views. For Processing FASTQ files after fastq-dump
Popular Question 5 months ago, created a question with more than 1,000 views. For VCF to BCF file conversion
Popular Question 8 months ago, created a question with more than 1,000 views. For VCF to BCF file conversion
Popular Question 10 months ago, created a question with more than 1,000 views. For VCF to BCF file conversion
Popular Question 10 months ago, created a question with more than 1,000 views. For VCF to BCF file conversion
Popular Question 13 months ago, created a question with more than 1,000 views. For VCF to BCF file conversion
Supporter 15 months ago, voted at least 25 times.
Student 17 months ago, asked a question with at least 3 up-votes. For P-Value calculation from iHS and XP-EHH scores
Popular Question 17 months ago, created a question with more than 1,000 views. For VCF to BCF file conversion
Popular Question 2.9 years ago, created a question with more than 1,000 views. For VCF to BCF file conversion

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