Hi there,

I have a list of variants (in vcf format) called across two samples. I want to use multiple criteria to select a subset of these variants. 

For example, I want to select "G" to "A" or "C" to "T" changes, since I'm only interested in these two specific type of SNPs.

Also, I want these SNPs have certain GT call combinations in the two samples: "0/1" GT call for sample 1 and "1/1" GT call for sample 2; or cannot be "1/1" for both samples at the same time. 

What's the best way to achieve this? I had difficulty combining these criteria. 

Thanks!

George

class: CollapsedVCF 
dim: 309482 2 
rowRanges(vcf):
  GRanges with 5 metadata columns: paramRangeID, REF, ALT, QUAL, FILTER
info(vcf):
  DataFrame with 17 columns: INDEL, IDV, IMF, DP, VDB, RPB, MQB, BQB, MQSB, SGB, MQ0F, ICB, HOB, AC, AN, DP4, MQ
info(header(vcf)):
         Number Type    Description                                                                                         
   INDEL 0      Flag    Indicates that the variant is an INDEL.                                                             
   IDV   1      Integer Maximum number of reads supporting an indel                                                         
   IMF   1      Float   Maximum fraction of reads supporting an indel                                                       
   DP    1      Integer Raw read depth                                                                                      
   VDB   1      Float   Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better),Version
   RPB   1      Float   Mann-Whitney U test of Read Position Bias (bigger is better)                                        
   MQB   1      Float   Mann-Whitney U test of Mapping Quality Bias (bigger is better)                                      
   BQB   1      Float   Mann-Whitney U test of Base Quality Bias (bigger is better)                                         
   MQSB  1      Float   Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)                            
   SGB   1      Float   Segregation based metric.                                                                           
   MQ0F  1      Float   Fraction of MQ0 reads (smaller is better)                                                           
   ICB   1      Float   Inbreeding Coefficient Binomial test (bigger is better)                                             
   HOB   1      Float   Bias in the number of HOMs number (smaller is better)                                               
   AC    A      Integer Allele count in genotypes for each ALT allele, in the same order as listed                          
   AN    1      Integer Total number of alleles in called genotypes                                                         
   DP4   4      Integer Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases                 
   MQ    1      Integer Average mapping quality                                                                             
geno(vcf):
  SimpleList of length 2: GT, PL
geno(header(vcf)):
      Number Type    Description                              
   GT 1      String  Genotype                                 
   PL G      Integer List of Phred-scaled genotype likelihoods