Question: Mpile up output
1
gravatar for d.angra
3.4 years ago by
d.angra50
United Kingdom
d.angra50 wrote:

Hi 

I am using Mpileup using SAM tools version 1.2+htslib-1.2.1 to generate variants. The tool works fine and gives me an output in VCF version 4.2. However there is no such description of VCF fromat file as in other VCF version 4.1. So it is hard to understand the file.Still I go convert vcf to tab delimit my file and I can see samples with all the details

QUAL FILTER BQB DP I16 IDV IMF MQ0F MQB MQSB QS RPB SGB VDB INDEL SAMPLE PL

 etc. But When I apply filter on VCF file for quality or REF  not equal to ALT allele, the number of lines comes to half of original file, but when I tab limit  this vcf file I can see nothing except the first line with information. I dont understand whats going on. How to apply filter is my question so that I can only get SNPs from a list of variants ??

I have tried using the same dataset with FREE BAYES and it runs well.

I have seen something very peculiar in freebayes also. When I filter my vcf file with one aspect I get an output and when using this as an input for a second step I get reults but on tab delimiting I see all information columns merged together.Is there some thing wrong with VCF tool manipulation to convert to tab delimit. Or is there anythiny I am doing wrong?

Any help will be appreciated.

 

Viva

samtools • 988 views
ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by d.angra50
0
gravatar for Jennifer Hillman Jackson
3.4 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Would you please send this in a bug report? Note the different VCF outputs by dataset # in the comments plus include a link to this post. 

Thanks! Jen, Galaxy team

ADD COMMENTlink written 3.4 years ago by Jennifer Hillman Jackson25k
0
gravatar for d.angra
3.4 years ago by
d.angra50
United Kingdom
d.angra50 wrote:

Hello Jen,

I don't get bug report for these jobs as they get completed but when I view the datasets I observe these differences to the normal files.

I have seen the different VCF outputs, they are all VCFversion 4.2. But Freebayes output is in VCF  version 4.1. You are very welcome to see my history items to have a further information about this problem.

 

Regards

Viva

ADD COMMENTlink written 3.4 years ago by d.angra50
0
gravatar for d.angra
3.4 years ago by
d.angra50
United Kingdom
d.angra50 wrote:

Hi Jen

I am sending you the link to vcf output dataset which has been tab-delimited .

https://usegalaxy.org/datasets/bbd44e69cb8906b594c1b9ce306a88b8/display/?preview=True

But when I visualise it under preview in galaxy it gives a tabular look as any other tab delimited file.

 

Hope this might help you understand much better what my query is. Sorry for this

 

Regards

Viva

ADD COMMENTlink written 3.4 years ago by d.angra50
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