User: tarek.mohamed
tarek.mohamed • 270
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Posts by tarek.mohamed
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Comment:
C: impute2 output files to vcf
... I was able to get the genotypes as follows,
re-ran impute2 with flag `-phase` to generate haplotypes file. Then I used shapeit to convert get vcf files
shapeit -convert --input-haps impute2 --output-vcf impute2.vcf
How can I keep the raw posterior-probability triplets in the .gen file ("GP")? ...
written 13 months ago by
tarek.mohamed • 270
1
vote
1
answer
580
views
1
answers
Comment:
C: impute2 output files to vcf
... I re-ran impute2 with flag `-phase` to generate haplotypes file. Then I used shapeit to convert get vcf files
shapeit -convert --input-haps impute2 --output-vcf impute2.vcf ...
written 13 months ago by
tarek.mohamed • 270
0
votes
1
answer
580
views
1
answers
Comment:
C: impute2 output files to vcf
... How can I convert it using shapeit.
I did not see that Gen format is an input option in shapeit convert?
Thanks ...
written 13 months ago by
tarek.mohamed • 270
0
votes
1
answer
580
views
1
answers
Comment:
C: impute2 output files to vcf
... My impute2 file has a different identifier than what is required by bcftools to work (CHROM:POS_REF_ALT). ...
written 13 months ago by
tarek.mohamed • 270
4
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1
answer
580
views
1
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... Hi All,
I need to know how can I deal with impute2 output file, how can I convert them to vcf files or is there a way by which I get vcf files as an impute2 output
I has a vcf file with a gwas dataset for which I need to run impute2.
I converted the vcf file into plink (bed,bim,fam) fromat, then ...
written 13 months ago by
tarek.mohamed • 270
• updated
13 months ago by
_r_am ♦ 32k
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... Hi,
I have the vcf file, but I wonder how can I do the actual error rate analysis?
Thanks ...
written 20 months ago by
tarek.mohamed • 270
2
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988
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... Dear All,
How can I analyze the error rate of my Minion reads?
how to calculate the error rate of insertion, deletion and Substitutions?
thankT ...
written 20 months ago by
tarek.mohamed • 270
• updated
19 months ago by
Biostar ♦♦ 20
4
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... Hi,
I have six vcf files (cases vs control) that contain structural variants with variable length from nanopore sequence run. These vcf files were generated using NGMLR aligner followed by sniffle.
What is the best way/tool to compare these files?
Thanks
Tarek ...
written 2.2 years ago by
tarek.mohamed • 270
• updated
2.2 years ago by
WouterDeCoster ♦ 45k
0
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1
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... Thanks for the reply!
This command will exclude 90% of reads at a position. Which reads will be excluded, is it a random process?
Do I have any power to select on what bases these reads will be excluded? as for example keep the reads with highest mapping quality or base quality scores?
Since the c ...
written 2.4 years ago by
tarek.mohamed • 270
1
vote
1
answer
550
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1
answer
... Hi,
I have a bam file includes a single gene sequence with huge coverage (> 5000X) from which I want to call snps. I have several snps previously identified in my sample which I am going to use as control to test my pipeline.
From my original bam file , I want to generate some bam files with dif ...
written 2.4 years ago by
tarek.mohamed • 270
• updated
2.4 years ago by
WouterDeCoster ♦ 45k
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