Can I provide my snp_VCF file instead of generating it from extract_snps.py?

[Jie Liu]

Hi everyone,

If I have a snp vcf file for allele-specific mode, however it was not generated from extract_snps.py, what should I do to reformat it for HiC-Pro analysis?

Those annotation line are necessory for HiC-Pro? For example,

##FILTER=<ID=PASS,Description="Allfilterspassed">

What about other columns like INFO?

Here is an example file generated from extract_snps.py

-----

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 129P2_OlaHsd-PWK_PhJ-F1
chr1    3000321 rs583231582     G       T       999     PASS    DP=1295;DP4=767,500,14,14;CSQ=T||||intergenic_variant||||||||   GT      0|1
chr1    3001313 rs582038162     C       T       999     PASS    DP=1661;DP4=794,750,63,54;CSQ=A||||intergenic_variant||||||||,T||||intergenic_variant||||||||   GT      0|1

-------

Here is part of my vcf file, we call snps and filter after we did whole-genome sequence.

chr1    3000287 .       A       G       635.03  PASS    AC=2;AF=1.00;AN=2;DP=20;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=31.37;QD=31.75;SOR=0.892        GT:AD:DP:GQ:PL  1/1:0,20:20:60:649,60,0
chr1    3000321 .       G       T       976.03  PASS    AC=2;AF=1.00;AN=2;DP=22;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.54;QD=25.36;SOR=1.609        GT:AD:DP:GQ:PL  1/1:0,22:22:66:990,66,0

Thanks!

[nservant]

Hi,

Sorry for the delay. Yes I think it should work.

So finally, did you try it ?

N