User: SOHAIL

gravatar for SOHAIL
SOHAIL90
Reputation:
90
Status:
Trusted
Location:
Beijing Institute of Genomics, CAS.
Last seen:
1 month, 3 weeks ago
Joined:
2 years, 4 months ago
Email:
m*****************@live.com

Posts by SOHAIL

<prev • 53 results • page 1 of 6 • next >
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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 8 weeks ago by SOHAIL90
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Comment: C: Switch the position of REF/ALT alleles based on AA (ancestral allele) annotation
... Problem solved...! Thanks ...
written 3 months ago by SOHAIL90
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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 3 months ago by SOHAIL90
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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 3 months ago by SOHAIL90
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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 3 months ago by SOHAIL90 • updated 3 months ago by Pierre Lindenbaum100k
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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 8 months ago by SOHAIL90
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Comment: C: Generate Consensus sequence from BAM file
... Hi @Dan, thanks for the answer.. can you suggest any way to run samtools faster? ...
written 9 months ago by SOHAIL90
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Answer: A: Generate Consensus sequence from BAM file
... Hi, I had a problem in running samtools/bcftools while generating consensus sequence. my command line was: samtools mpileup -C50 -uf REF.fa BQSR_AAGC0220.bam | bcftools view -c - | perl vcfutils.pl vcf2fq -d 8 -D 100 | gzip > AAGC0220.fq.gz later as i learnt bcftools modified the options f ...
written 9 months ago by SOHAIL90
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Comment: C: Generate Consensus sequence from BAM file
... Hi @Shengweima thanks for the help.. it works on small dataset.. can you please give an idea how much time it takes normally for 30X genome.? i am running my job from last 20 hours.. ...
written 9 months ago by SOHAIL90
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Generate Consensus sequence from BAM file
... Hi everyone, I want to generate diploid consensus sequence for one human individual from BAM file for PSMC analysis purposes. my command line is: samtools mpileup -C50 -uf REF.fa BQSR_AAGC0220.bam | bcftools view -c - | perl vcfutils.pl vcf2fq -d 8 -D 100 | gzip > AAGC0220.fq.gz The command ru ...
psmc samtools mpileup written 9 months ago by SOHAIL90

Latest awards to SOHAIL

Popular Question 3 months ago, created a question with more than 1,000 views. For VCF to BCF file conversion
Popular Question 3 months ago, created a question with more than 1,000 views. For VCF to BCF file conversion
Popular Question 6 months ago, created a question with more than 1,000 views. For VCF to BCF file conversion
Supporter 8 months ago, voted at least 25 times.
Student 10 months ago, asked a question with at least 3 up-votes. For P-Value calculation from iHS and XP-EHH scores
Popular Question 10 months ago, created a question with more than 1,000 views. For VCF to BCF file conversion
Popular Question 2.3 years ago, created a question with more than 1,000 views. For VCF to BCF file conversion

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