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Question: MAF in VCF file, where is it?
0
gravatar for ginlucks
3.8 years ago by
ginlucks • 10
European Union
ginlucks • 10 wrote:

Hi all

I'm using galaxy and I need to know allele frequency (MAF, minor frequency allele) for each SNP or variant.

I click on "view data" but it show as frequency's value (AF=)  only 1,00 or 0,50

I wonder where I'm going wrong..

 
af vcf maf • 2.2k views
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modified 3.8 years ago • written 3.8 years ago by ginlucks • 10
0
gravatar for Jennifer Hillman Jackson
3.8 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Please see the tool "NGS: VCF Manipulation -> VCFfixup" on the public Main Galaxy instance. It is also available in the tool shed for use in a local/cloud.

Best, Jen, Galaxy team
ADD COMMENT • link written 3.8 years ago by Jennifer Hillman Jackson ♦ 25k
0
gravatar for ginlucks
3.8 years ago by
ginlucks • 10
European Union
ginlucks • 10 wrote:

Hello, thank you for answer.

I used "NGS: VCF Manipulation -> VCFfixup" but problem persists.

Any other suggest?

 

thank you in advance.
ADD COMMENT • link written 3.8 years ago by ginlucks • 10

An alternate tool is "NGS: Variant Analysis -> Variant Annotator" (note this is NOT the tool in the GATK tool group). This take in a specific type of VCF file (stranded). See the comments in the tool's help for more details. Thanks! Jen, Galaxy team

ADD REPLY • link written 3.8 years ago by Jennifer Hillman Jackson ♦ 25k
0
gravatar for ginlucks
3.8 years ago by
ginlucks • 10
European Union
ginlucks • 10 wrote:

I have try to use some tools as Variant annotator or MAF exploit but it shows me these errors

Fatal error: Exit code 1 () Error: Input file does not seem to have a proper header line. Adding an artificial header..Traceback (most recent call last): File "/galaxy/main/shed_tools/toolshed.g2.bx.psu.edu/repos/boris/hetbox/8d2c4c11fd8f/hetbox/hetbox


Fatal error: Exit code 1 () Error in input VCF: Incorrect variant data format (must contain a single '='). Failed on line: chrM 72 . T C 123.03 LowCoverage ABHom=1.00;AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=4

 

Is there a problem with VCF file?
ADD COMMENT • link modified 3.8 years ago • written 3.8 years ago by ginlucks • 10
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