FelixKrueger
commented
3 years ago Hi Pui,
I theory you should be able use this information as to construct a genome, but you will need to adhere to the same rules that the script uses internally.
First of all, you cannot use / characters in names as it would probably do bad things. I would recommend an underscore _ instead, so maybe:
--strain JF1_Ms
Next, the SNPs will need to be contained within a folder called:
SNPs_JF1_Ms
inside there, the script expects one file per chromosome, e.g. like so:
chr10.txt
chr11.txt
chr12.txt
chr13.txt
chr14.txt
chr15.txt
chr16.txt
chr17.txt
chr18.txt
chr19.txt
chr1.txt
chr2.txt
chr3.txt
chr4.txt
chr5.txt
chr6.txt
chr7.txt
chr8.txt
chr9.txt
chrMT.txt
chrX.txt
chrY.txtSo you will have to split your tsv file by chromosome. And finally, these file need to adhere to the following format:
>10
42459235 10 3101362 1 G/C 1/1:101:31:0:284,101,0:255,90,0:2:51:31:0,0,22,9:0:-0.69311:.:1
42459276 10 3102112 1 T/C 1/1:127:50:0:288,164,0:255,151,0:2:44:50:0,0,22,28:0:-0.693147:.:1
42459298 10 3102661 1 C/G 1/1:127:59:0:290,192,0,.,.,.:255,178,0,.,.,.:2:48:59:0,0,34,25:0:-0.693147:.:1
42459325 10 3103479 1 A/G 1/1:127:49:0:288,161,0:255,148,0:2:57:49:0,0,17,32:0:-0.693147:.:1
...where the first line is the name of the chromosome (like in a FastA file).
this is also explained in the option:
--skip_filtering This option skips reading and filtering the VCF file. This assumes that a folder named
'SNPs_<Strain_Name>' exists in the working directory, and that text files with SNP information
are contained therein in the following format: SNP-ID Chromosome Position Strand Ref/SNP
example: 33941939 9 68878541 1 T/GI believe column 6 is optional, but the first 5 need to be present. It is sufficient to put 1 as strand if the sequence is based relative to the top strand. So you will need to reformat your file just a little, and you should be able to run it. If you have no one to do this for you I might be able to help.
I hope this makes sense?
pplaw
Dear Felix,
My group is hoping to analyse some published data generated from a hybrid mouse train (C57BL/6J x JF1/Ms) in which SNP information for JF1/Ms is not available in the “mgp.v5.merged.indels.dbSNP142.normed.vcf.gz” vcf file from sanger institute website We have however managed to find the SNP info stored in a .tsv file for this strain in the following format:
Can I please check with you whether we can use this tsv file (or a reformatted version of this tsv file) for generation of the masked genome using the following command:
SNPsplit_genome_preparation --reference /ref_genome/mm10/ --strain JF1/Ms --skip_filtering
Many thanks!
Best, Pui