alachins
commented
9 months ago Hi chichi, RAiSD can handle this file size (I have tested it with input files of up to 65GB). The error you get means that not all SNPs in the same chromosome have the same length. RAiSD reads the expected SNP length from the very first SNP in each chromosome. Best regards, Nikos A.
On Thu, Dec 14, 2023 at 4:20 AM chichi @.***> wrote:
HI! Alachins I got a problem, when I deal with my snp vcf data. The question
When I am trying to use RAISD to detect the Sweep and positive selection sites with the population snp vcf file, which produced by the GATK pipleline, it give the following report. I have read the readme file carefully, while I still fail to deal with it. So would you please help me figure out what is the problem? many thanks to that some information
The vcf file is kind of large ~ 6 GB without zip. It contains 111 samples. It contains 15 Chromesomes (start with Chr01) and 2 contigs ( congtig01 ) my guess
Is this file too large for handle ? Yes, it is too confused for the hint information, so I leave this communt for you. Stilling working on it, thank for you response.
best ~ chichi the output information
RAiSD, Raised Accuracy in Sweep Detection This is version 2.9 (released in August 2020) Copyright (C) 2017, and GNU GPL'd, by Nikolaos Alachiotis and Pavlos Pavlidis Contact n.alachiotis/pavlidisp at gmail.com Command: /home/chichi/softwares/RAiSD/RAiSD -n test -I ../data/merge3_filter_variants_snp.vcf -f Samples: 111 Format: vcf var-exp: 1.0 sfs-exp: 1.0 ld-exp: 1.0
A pattern structure of 349525 patterns (max. capacity) and approx. 16 MB memory footprint has been created.
The pattern structure has been resized to 209715 patterns (max. capacity) and approx. 16 MB memory footprint.
ERROR: Wrong SNP size (L) found!
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chichizhao
HI! Alachins I got a problem, when I deal with my snp vcf data.
The question
When I am trying to use RAISD to detect the Sweep and positive selection sites with the population snp vcf file, which produced by the GATK pipleline, it give the following report. I have read the readme file carefully, while I still fail to deal with it. So would you please help me figure out what is the problem? many thanks to that
some information
The vcf file is kind of large ~ 6 GB without zip. It contains 111 samples. It contains 15 Chromesomes (start with Chr01) and 2 contigs ( congtig01 )
my guess
Is this file too large for handle ? Yes, it is too confused for the hint information, so I leave this communt for you. Stilling working on it, thank for you response.
best ~ chichi
the output information