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Longranger basic - phased vcf

Posted By: jpenalba, on Dec 4, 2018 at 8:21 AM

Hi,

 

I'm not sure if I am understanding this correctly but what order does the BX field in the phased vcf after running Longranger basic follow? According to this (https://support.10xgenomics.com/genome-exome/software/pipelines/latest/output/vcf) the first 10X barcodes should correspond the reads associated with the reference allele, then followed by all the barcodes corresponding to the alternate allele(s). Is that correct? So the phase does not matter (either 0|1 or 1|0) the first barcodes always correspond to the reference ('0')? Thanks in advance

 

Best,

Josh

4 Replies

Re: Longranger basic - phased vcf

Posted By: 10xDave, on Dec 4, 2018 at 12:03 PM

Hi Josh

 

Can you confirm which Long Ranger pipeline you are running? basic? wgs?

  

The longranger basic pipeline performs basic read and barcode processing including read trimming, barcode error correction, barcode whitelisting, and attaching barcodes to reads. It outputs barcode-attached reads either as FASTQ or unaligned BAM.  It does not perform phasing. The phased VCF docs you referred to should not apply.

 

Best,

Dave

 

https://support.10xgenomics.com/genome-exome/software/pipelines/latest/advanced/other-pipelines

 

Re: Longranger basic - phased vcf

Posted By: jpenalba, on Dec 4, 2018 at 12:19 PM
Hi Dave,

My mistake. Yes, I ran longranger wgs to produce this vcf.

Best,
Josh

Re: Longranger basic - phased vcf

Posted By: 10xDave, on Dec 4, 2018 at 4:59 PM

Hi Josh

 

Thanks for clarifying that you are running the wgs pipeline.

 

Q1: I'm not sure if I am understanding this correctly but what order does the BX field in the phased vcf after running Longranger basic follow? According to this (https://support.10xgenomics.com/genome-exome/software/pipelines/latest/output/vcf) the first 10X barcodes should correspond the reads associated with the reference allele, then followed by all the barcodes corresponding to the alternate allele(s). Is that correct?

 

A1: That is correct. The BX tag stores the 10x barcodes supporting each allele of the variant. The order is REF, ALT1, ALT2....

 

Q2: So the phase does not matter (either 0|1 or 1|0) the first barcodes always correspond to the reference ('0')? 

 

A2: Confirmed!

 

 

 

 

 

 

Re: Longranger basic - phased vcf

Posted By: jpenalba, on Dec 4, 2018 at 11:17 PM
Great! And thanks for the prompt response!

Best,
Josh