"Patched 0 SNPs total"

[hanbinlu]

Hi,

I use the strain variant data from mouse genome project and follow the document to patch and transform the reference mm10 genome to get CAST_EiJ genome. The log did not report any error but I could not get SNPs or indels at the end. Here is my commands

g2gtools vcf2vci  -s CAST_EiJ -o mgp.v6.vci  -p 35 -i strain_variants/mgp.v6.merged.norm.snp.indels.sfiltered.vcf.gz -f mm10.fa
g2gtools patch -c mgp.v6.vci.gz  -p 35  -i  mm10.fa -o mm10_patched.CAST.fa

Log
[g2gtools] Processing chr4...
[g2gtools] Processing chr7...
[g2gtools] Processing chr14...
[g2gtools] Processing chr10...
[g2gtools] Processing chr1...
[g2gtools] Processing chrX...
[g2gtools] Patched 0 SNPs total
[g2gtools] Patch complete: 00:01:26.50

The vcf file should be no problem since I used it to patch individual regions using bcftools before.

I really appreciate your help.

[kbchoi-jax]

It could be just error in the log. Could you open the vci file in text editor and look into it please?

[hanbinlu]

Hi,

The full log for vcf2vci

[g2gtools] VCF file: /Extension_HDD1/strain_variants/mgp.v6.merged.norm.snp.indels.sfiltered.vcf.gz
[g2gtools] Checking for index file, creating if needed...
[g2gtools] Fasta File: /Extension_HDD1/mgp.v6.vci
[g2gtools] Strain: CAST_EiJ
[g2gtools] Pass filter on: False
[g2gtools] Quality filter on: False
[g2gtools] Diploid: False
[g2gtools] Number of processes: 35
[g2gtools] Output VCI File: /Extension_HDD1/mgp.v6.vci
[g2gtools] Parsing VCF files...
[g2gtools] Processing Chromosome 1...
[g2gtools] Processing Chromosome 2...
[g2gtools] Processing Chromosome 4...
[g2gtools] Processing Chromosome 5...
[g2gtools] Processing Chromosome 3...
[g2gtools] Processing Chromosome 7...
[g2gtools] Processing Chromosome 6...
[g2gtools] Processing Chromosome 8...
[g2gtools] Processing Chromosome 11...
[g2gtools] Processing Chromosome 10...
[g2gtools] Processing Chromosome 9...
[g2gtools] Processing Chromosome 12...
[g2gtools] Processing Chromosome 13...
[g2gtools] Processing Chromosome 15...
[g2gtools] Processing Chromosome 16...
[g2gtools] Processing Chromosome 14...
[g2gtools] Processing Chromosome 17...
[g2gtools] Processing Chromosome MT...
[g2gtools] Processing Chromosome X...
[g2gtools] Processing Chromosome 19...
[g2gtools] Processing Chromosome 18...
[g2gtools] Processing Chromosome Y...
[g2gtools] Finalizing VCI file...
[g2gtools] Parsed 90,310,977 total lines
[g2gtools] VCI creation complete: 00:08:06.62

The vci seems fine to me and has 426398 (fewer than expected?)
##CREATION_TIME=08/13/2019 14:37:43
##INPUT_VCF=/Extension_HDD1/strain_variants/mgp.v6.merged.norm.snp.indels.sfiltered.vcf.gz
##FASTA_FILE=MM10.fa
##STRAIN=CAST_EiJ
##VCF_KEEP=False
##FILTER_PASSED=False
##FILTER_QUALITY=False
##DIPLOID=False
##PROCESSES=35
##CONTIG=chr1:195471971
##CONTIG=chr10:130694993
##CONTIG=chr11:122082543
##CONTIG=chr12:120129022
##CONTIG=chr13:120421639
##CONTIG=chr14:124902244
##CONTIG=chr15:104043685
##CONTIG=chr16:98207768
##CONTIG=chr17:94987271
##CONTIG=chr18:90702639
##CONTIG=chr19:61431566
##CONTIG=chr2:182113224
##CONTIG=chr3:160039680
##CONTIG=chr4:156508116
##CONTIG=chr5:151834684
##CONTIG=chr6:149736546
##CONTIG=chr7:145441459
##CONTIG=chr8:129401213
##CONTIG=chr9:124595110
##CONTIG=chrM:16299
##CONTIG=chrX:171031299
##CONTIG=chrY:91744698
#CHROM POS ANCHOR INS DEL FRAG
1 3000019 G . A 3000019
1 3000020 . T A .
1 3000023 . C A .
1 3000097 CTT TTTTTTTTTT . 80

[juhomon]

You seem to have different chr names in your contigs and in coordinates (chr1 vs 1).
##CONTIG=chr1:195471971
1 3000019 G . A 3000019

Have you checked wether chr names of the contigs in your VCF are different format from the coordinate lines in the vcf? This helped me.