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Search: Posts Made By: liying
Forum: Bioinformatics 12-26-2011, 04:34 AM
Replies: 4
Views: 2,268
Posted By liying
hi,jeny I do have the index file. I may try...

hi,jeny
I do have the index file.
I may try perl version.
Thanks.

------------

I have tried the BreakDancerMax.pl. Unfortunately, the output was empty expect #header, too. And there was...
Forum: Bioinformatics 12-21-2011, 10:31 PM
Replies: 4
Views: 2,268
Posted By liying
Did you figure this out? And if you did, could...

Did you figure this out? And if you did, could you share the solution?
I also encountered this problem.
Thanks a lot!
Forum: Bioinformatics 09-26-2011, 09:15 PM
Replies: 2
Views: 1,481
Posted By liying
Enter: vcfutils.pl varFilter The detail will...

Enter:
vcfutils.pl varFilter
The detail will be shown on screen.
-d 10 is what you want.
Forum: Bioinformatics 09-26-2011, 09:13 PM
Replies: 6
Views: 3,637
Posted By liying
Heisman,thanks! why use -g and -u together?...

Heisman,thanks!

why use -g and -u together? We used piping, so it should be -u.

samtools mpileup
-g Compute genotype likelihoods and output them in the binary call format (BCF).
-u ...
Forum: Bioinformatics 09-26-2011, 09:03 PM
Replies: 6
Views: 3,637
Posted By liying
Heisman,thank you very much! My vcf file don't...

Heisman,thank you very much!
My vcf file don't have any header. Could you post you command?

My command:
samtools mpileup -A -q 20 -Q 13 -C 50 -uf Egrandis_162.fa 2.rmdup.bam | bcftools view...
Forum: Bioinformatics 09-26-2011, 06:26 PM
Replies: 11
Views: 3,664
Posted By liying
I always think so. And the insert size is...

I always think so. And the insert size is anomalous or not should depend on the mapping option you set.

Such as: bwa sampe -a

This is my personal guess.
Forum: Bioinformatics 09-26-2011, 06:12 PM
Replies: 6
Views: 3,637
Posted By liying
It turns out be a version error. We didn't change...

It turns out be a version error. We didn't change $PATH of bcftools when updata samtools.
Now the result is

scaffold_1 8463589 . T C 59.3 . ...
Forum: Bioinformatics 09-26-2011, 01:42 AM
Replies: 6
Views: 3,637
Posted By liying
How samtools computes AF1?

Hi,Sorry to ask basic.

I get such vcf by smtools mpileup, But can't understand it.

scaffold_1 8463589 . T C 47 . ...
Forum: Bioinformatics 09-23-2011, 12:02 AM
Replies: 3
Views: 2,099
Posted By liying
Foget it. I'm a fool. I shouldn't use -6 option...

Foget it. I'm a fool. I shouldn't use -6 option after adding -I in bwa.
Well, it's a good thing that I'm wrong and samtools is right, so I can use it...
Forum: Bioinformatics 09-18-2011, 08:05 PM
Replies: 3
Views: 2,099
Posted By liying
Thanks for you reply. I'm sure these SNPs...

Thanks for you reply.
I'm sure these SNPs should pass my fliter. The MAPQ, baseQ and depth is good enough. And no matter how low threshold be set, I did not got any SNPs anyway.
As -B option was...
Forum: Bioinformatics 09-15-2011, 12:51 AM
Replies: 3
Views: 2,099
Posted By liying
strange results of samtools

Hi, everyone!
I'm dealing with 14 sets of 81*2 data. After mapping them to reference genome by bwa 0.5.9-r16, I try to call variants using samtools 0.1.18. The strange thing is that all the...
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