Is varaint transform create empty tables please help

[hze...@gmail.com]

Dear Life sciences team

I have applied variant transforms to some vcf files it end up as empty tables is my task is completed correctly i want to find ti/tv ratio and (0 Bytes)

but my question is if it created empty tables how i am going to find ti/tv query using big query 

best regards

Thanks in advance

Haroon zeb

[Saman Vaisipour]

Hi Haroon,

VariantTransforms creates multiple output tables, one per chromosome as per default sharing config file. So if your input VCF file only contains variants on, say Chromosomes 1 and 3, then all output tables except for __chr1 and __chr3 will be empty.

Hope this helps,

--Saman

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Saman Vaisipour |

Software Eng |

sam...@google.com |

519-513-5756

 

[hze...@gmail.com]

Dear Life sciences team

variant transform generates tables _chr1,chr10,chr11,chr12chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chr3,chr4 ,chr5, chr6,chr7,chr8,chr9,chr X, chr Y ,_residual and _sample

it did not generate chr2 so what is wrong is my vcf files are different tell me about among all tables were empty, but _residual is nonempty so can we say that _residual is the result we aim at.

secondly tell me in the big query,in the case of variant transforms 

i created a dataset  but I did not create a table instead I named the big query table  is it good practice 

Thanks in advance

haroon zeb

[Saman Vaisipour]

Please see my reply inline below:

On Wed, Mar 10, 2021 at 1:14 PM hze...@gmail.com <hze...@gmail.com> wrote:

Dear Life sciences team

variant transform generates tables _chr1,chr10,chr11,chr12chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chr3,chr4 ,chr5, chr6,chr7,chr8,chr9,chr X, chr Y ,_residual and _sample

Are you sure chr2 is missing? VariantTransforms creates output tables as an atomic operation, meaning that either all or none of them are created.

it did not generate chr2 so what is wrong is my vcf files are different tell me about among all tables were empty, but _residual is nonempty so can we say that _residual is the result we aim at.

 Again if you refer back to default sharing config file, you will see that we instruct VariantTransforms to store all variants with CHROM value of "1" or "chr1" in __chr1 table, "2" or "chr2" in __chr2 table, ... and "chry" or "chrY" or "y" or "Y" in __chry table. All remaining variants would be stored in a __residual table. If your input VCF file has different CHROM values (for example "C1", "C2", "C3", ...) you can modify the config file so each chromosome's variants will be stored in the right table. You could find this by running the following query on the residual table you have:

SELECT DISTINCT(reference_name) FROM `YOUR_TABLE_NAME__residual`

secondly tell me in the big query,in the case of variant transforms 

i created a dataset  but I did not create a table instead I named the big query table  is it good practice 

Exactly, that is the best practice; as per our documentations if set  --output_table my_table then you will get my_table__chr1, my_table__chr2, ..., my_table__chry

 

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