FelixKrueger
commented
3 years ago Hi Hemant,
If I understand you correctly, you've made up the SNP files for strain JF1_MsJ yourself? In order to get the required files for 129S1_SvImJ you should be able to simply run SNPsplit for the just that strain (with --full_sequence) which is required as the base genome for the second strain.
In theory, as long as you've got the latest version of SNPsplit, it should work pretty much as described here (#41):
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_MsNext, the SNPs will need to be contained within a folder called:
SNPs_JF1_Msinside 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 do you have this SNP_folder? Do the files in there look like described above?
I just checked the Sanger FTP site and noticed that there is an even newer version of the MGP file, version 7 (ftp://ftp-mouse.sanger.ac.uk/REL-2004-v7-SNPs_Indels/mgp_REL2005_snps_indels.vcf.gz). Initially we agreed to wait with adapting the genome preparation script until there is a new, official release (in Current_SNPs, version 5 is still the one listed). There hasn't been an official new release since 2015 though, and v7 is from May 2020. Maybe it would be worth for me to take a look at whether it is feasiblet to support the v7 file, what do you think?
mgp_REL2005_snps_indels.vcf.gz
Hemantcnaik
Hello, Great tool I am trying with the v6 version of VCF( ftp://ftp-mouse.sanger.ac.uk/REL-1807-SNPs_Indels/mgp.v6.merged.norm.snp.indels.sfiltered.vcf.gz ) because of desired genome its not present in V5,
I tried with seperate vcf file for 129S1 and JF1 and tried to followed steps in issues #31 , #41 still get empty files as a output command I tried as below
SNPsplit_genome_preparation --reference /media//SNPsplit/ --skip_filtering --dual_hybrid --strain 129S1_SvImJ --strain2 JF1_MsJ
output
Summary 0 Ns were newly introduced into the N-masked genome for strain 2 [JF1_MsJ] in total Determining new Ref [129S1_SvImJ] and SNP [JF1_MsJ] annotations
Writing 129S1_SvImJ specific SNPs (relative to the GRCm38 reference) to >>129S1_SvImJ_specific_SNPs.GRCm38.txt<< Writing JF1_MsJ specific SNPs (relative to the GRCm38 reference) to >>JF1_MsJ_specific_SNPs.GRCm38.txt<< Writing SNPs in common between 129S1_SvImJ and JF1_MsJ (relative to the GRCm38 reference) to >>129S1_SvImJ_JF1_MsJ_SNPs_in_common.GRCm38.txt<< Writing all new SNPs >>129S1_SvImJ/JF1_MsJ to >>all_JF1_MsJ_SNPs_129S1_SvImJ_reference.based_on_GRCm38.txt<<
Expected SNP file [all_SNPs_129S1_SvImJ_GRCm38.txt.gz] for strain 129S1_SvImJ did not exist! Please make sure that it is present in the current working directory