Filter 2 mapped VCF files so the "POS" are the same?

Question

[JBC]

I have two VCF files from different individuals. They are both mapped and have a number of non-overlapping positions. Is there a way to filter then so only the overlapping POS remain in the file?

File 1:

  #CHROM    POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  P1
  NW_014726.1   404 .   A   G   225 .   DP=15;VDB=0.310396;SGB=-0.686358;MQSB=0.640197;MQ0F=0;AC=2;AN=2;DP4=0,0,7,7;MQ=43   GT:PL   1/1:255,42,0
    NW_014726.1 495 .   T   C   225 .   DP=16;VDB=0.351783;SGB=-0.689466;MQSB=0.948436;MQ0F=0;AC=2;AN=2;DP4=0,0,6,10;MQ=39  GT:PL   1/1:255,48,0
    NW_014726.1 542 .   T   G   225 .   DP=16;VDB=0.909865;SGB=-0.688148;MQSB=0.959011;MQ0F=0;AC=2;AN=2;DP4=0,0,8,7;MQ=41   GT:PL   1/1:255,45,0
    NW_014726.1 722 .   G   A   225 .   DP=24;VDB=0.680279;SGB=-0.692352;MQSB=0.769328;MQ0F=0;AC=2;AN=2;DP4=0,0,8,13;MQ=40  GT:PL   1/1:255,63,0
    NW_014726.1 750 .   G   C   225 .   DP=22;VDB=0.501443;SGB=-0.692352;MQSB=0.95645;MQ0F=0;AC=2;AN=2;DP4=0,0,7,14;MQ=39   GT:PL   1/1:255,63,0

File 2:

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  M2
NW_014726.1 404 .   A   G   225 .   DP=14;VDB=0.237864;SGB=-0.683931;MQSB=0.679965;MQ0F=0;AC=2;AN=2;DP4=0,0,5,8;MQ=43   GT:PL   1/1:255,39,0
NW_014726.1 495 .   T   C   225 .   DP=15;VDB=0.67567;SGB=-0.686358;MQSB=0.939413;MQ0F=0;AC=2;AN=2;DP4=0,0,4,10;MQ=39   GT:PL   1/1:255,42,0
NW_014726.1 530 .   T   G   225 .   DP=16;VDB=0.650373;SGB=-0.686358;MQSB=0.411112;MQ0F=0;AC=2;AN=2;DP4=0,0,9,5;MQ=42   GT:PL   1/1:255,42,0
NW_014726.1 745 .   G   A   225 .   DP=18;VDB=0.178812;SGB=-0.690438;MQSB=1;MQ0F=0;AC=2;AN=2;DP4=0,0,6,11;MQ=41 GT:PL   1/1:255,51,0
NW_014726.1 750 .   G   C   206 .   DP=17;VDB=0.787081;SGB=-0.680642;RPB=0.893597;MQB=0.031048;MQSB=1;BQB=0.965874;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=2,3,4,8;MQ=41 GT:PL   0/1:239,0,115

The output I am looking for would remove the POS that are not in common and would look like this:

File 1:

  #CHROM    POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  P1
  NW_014726.1   404 .   A   G   225 .   DP=15;VDB=0.310396;SGB=-0.686358;MQSB=0.640197;MQ0F=0;AC=2;AN=2;DP4=0,0,7,7;MQ=43   GT:PL   1/1:255,42,0
    NW_014726.1 495 .   T   C   225 .   DP=16;VDB=0.351783;SGB=-0.689466;MQSB=0.948436;MQ0F=0;AC=2;AN=2;DP4=0,0,6,10;MQ=39  GT:PL   1/1:255,48,0
    NW_014726.1 750 .   G   C   225 .   DP=22;VDB=0.501443;SGB=-0.692352;MQSB=0.95645;MQ0F=0;AC=2;AN=2;DP4=0,0,7,14;MQ=39   GT:PL   1/1:255,63,0

File 2:

   #CHROM   POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  M2
    NW_014726.1 404 .   A   G   225 .   DP=14;VDB=0.237864;SGB=-0.683931;MQSB=0.679965;MQ0F=0;AC=2;AN=2;DP4=0,0,5,8;MQ=43   GT:PL   1/1:255,39,0
    NW_014726.1 495 .   T   C   225 .   DP=15;VDB=0.67567;SGB=-0.686358;MQSB=0.939413;MQ0F=0;AC=2;AN=2;DP4=0,0,4,10;MQ=39   GT:PL   1/1:255,42,0
    NW_014726.1 750 .   G   C   206 .   DP=17;VDB=0.787081;SGB=-0.680642;RPB=0.893597;MQB=0.031048;MQSB=1;BQB=0.965874;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=2,3,4,8;MQ=41 GT:PL   0/1:239,0,115

I tried using

bcftools merge

with the hope of just filtering a single file, but i keep running into problems, so no I am looking for a way to filter the individuals files based on the positions in the other.

Looking for any solution in R, BCFtools/VCFtools, or whatever combination of awk, grep, ... works.

[Pierre Lindenbaum]

use bcftools isec

Answer 1

[JBC]

I found a solution! In case anyone else is trying to do the same thing, I used bedtools:

bedtools intersect -sorted -a File1.vcf -b File2.vcf > NewFile1.vcf

Where NewFile1.vcf is File1.vcf with POS removed that are not in File2.vcf

[Pierre Lindenbaum]

this is not want you asked for. I you have any indel in your VCF1, it might overlap a variant in VCF2 while not having the same POS.

[JBC]

OK. I did not know that. But I did already filter out all indels with:

> vcftools  --remove-indels

Does that get around the problem?