chr prefix AND beagle failed

[zxx0902]

chr prefix AND beagle failed

[jcesar101]

Hi,

first of all thank you for using the Battenberg package. I'll try to help you with these problems.

1. The change is correct and the analysis type (-a) should be "paired".
2. These files should contain the chromosome names with the chr prefix. Could you please check the impute_info.txt on your environment, as this is where that information is retrieved from for this step.
3. Depending on the Battenberg version (or branch), the default value for the genome build is "hg19", you can explicitly set the required build with the command line parameter -g (or --ref_genome_build), e.g., -g hg38
4. Could you please check if the chromosome names in the generated vcf files contain the chr prefix or not? This might be related to the problems above, or to some other reference files not consistent with the rest in terms of the chr prefix

[zxx0902]

Hi
Firstly,Thanks for you suggestion and so quickly to reply my question.
Yestoday, i check all hg38 reference file form *_chr.zip. I found that chromosome name don't contain chr prefix in chrN.1kg.phase3.v5a_GRCh38nounref.vcf.gz of beagle. Then, i add the prefix to all file in chrN.1kg.phase3.v5a_GRCh38nounref.vcf.gz .So The second and fourth problem were solved.I can get corresponding file without error message.

About question 3:
I think i set value of ref_genome_build to hg38 in battenberg_wgs. R. the code as follow:

library(Battenberg)
library(optparse)
........
GENOMEBUILD = "hg38"
USEBEAGLE = T
......
} else if (GENOMEBUILD=="hg38") {
BEAGLE_BASEDIR = "/mypath/Battenberg_reference"
GENOMEBUILD = "hg38"
IMPUTEINFOFILE = file.path(BEAGLE_BASEDIR, "imputation/impute_info_1.txt")
G1000ALLELESPREFIX = file.path(BEAGLE_BASEDIR, "1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_")
G1000LOCIPREFIX = file.path(BEAGLE_BASEDIR, "1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_loci_")
GCCORRECTPREFIX = file.path(BEAGLE_BASEDIR, "GC_correction_hg38/1000G_GC_")
REPLICCORRECTPREFIX = file.path(BEAGLE_BASEDIR, "RT_correction_hg38/1000G_RT_")
PROBLEMLOCI = file.path(BEAGLE_BASEDIR, "probloci/probloci.txt.gz")

    BEAGLEREF.template = file.path(BEAGLE_BASEDIR, "beagle_chr/CHROMNAME.1kg.phase3.v5a_GRCh38nounref.vcf.gz")
    BEAGLEPLINK.template = file.path(BEAGLE_BASEDIR, "beagle_chr/plink.CHROMNAME.GRCh38.map")
    BEAGLEJAR = file.path(BEAGLE_BASEDIR, "beagle_chr/beagle.08Feb22.fa4.jar")

    CHROM_COORD_FILE = "/public/xxzhang/01.Project_LungCancer_WGS/02.Battenberg/Battenberg_reference/chromosome_coordinates_hg38_chr.txt"

If i use hg19 version,i think i will get the error message .eg. can't find battenberg_1000genomesloci2012_v3/1000genomesAlleles2012_chrN*. So i think i use the right reference version . also get the same annotation with GRCh37 in the LC_141_3_beagle5_input_chrchrN.txt

##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##reference=GRCh37
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMP001
chr1 3727147 . C T . PASS . GT 0/0
chr1 3728241 . A G . PASS . GT 0/1
chr1 3728294 . G C . PASS . GT 0/0

Do I need to make any other changes to files for beagle_chr.zip(dowmloaded form [https://ora.ox.ac.uk/objects/uuid :08e24957-7e76-438a-bd38-66c48008cf52]) ? or maybe I missed the some steps?

New question:
I get the warning message and i don't know if this affect to my results?
1: In diff(as.numeric(SNPpos[, 1])) : NAs introduced by coercion
2: The path argument of write_tsv() is deprecated as of readr 1.4.0.
ℹ Please use the file argument instead.
ℹ The deprecated feature was likely used in the Battenberg package.
Please report the issue to the authors

battenberg_wgs.R.txt
Battenberg_LC_141_1.out.txt

[jcesar101]

Hi!,

regarding the incorrect reference in the beagle5_input_ files, I checked that section of the code in detail, and is in fact keeping the default value for the reference genome build (hg19). This will be fixed in the next release of Battenberg, but it can be safely ignored as these are informative fields, unless you need sharing these intermediate files, in which case they should be edited to state the right genome build. No further changes are needed.

Regarding your new questions, both warning messages can be safely ignored. The new release of Battenberg will also include some changes to prevent these warnings from happening at the end.

[zxx0902]

Thanks for your help