Only output SNPs in bcftools

1

Hi, I have called SNPs using bcftools v1.8 using the following code

$ bcftools mpileup --threads 4 --output-type b -f reference.fa -o AS.merged.bcf AS.merged.bam
$ bcftools call --threads 4 -v -m -O z -o AS.variants.vcf.gz AS.merged.bcf

I got the following using rtg vcfstats

Location                     : AS.variants.vcf.gz
Failed Filters               : 0
Passed Filters               : 62280442
SNPs                         : 60581916
MNPs                         : 0
Insertions                   : 789867
Deletions                    : 908517
Indels                       : 142
Same as reference            : 0
SNP Transitions/Transversions: 1.74 (68137348/39175931)
Total Het/Hom ratio          : 0.31 (14805670/47474772)
SNP Het/Hom ratio            : 0.30 (13998666/46583250)
MNP Het/Hom ratio            : - (0/0)
Insertion Het/Hom ratio      : 0.91 (376478/413389)
Deletion Het/Hom ratio       : 0.90 (430384/478133)
Indel Het/Hom ratio          : - (142/0)
Insertion/Deletion ratio     : 0.87 (789867/908517)
Indel/SNP+MNP ratio          : 0.03 (1698526/60581916)

Now I'm trying to get a file with only the SNPs. I've tried both of the following:

$ bcftools call -t 4 -v -m -V indels -O z -o filtered.SNPs.vcf.gz AS.merged.bcf 
$ bcftools view -t 4 -V indels -O z -o filtered.SNPs.vcf.gz AS.merged.bcf

but both only output a file with a header and no variants at all

...
##bcftools_callCommand=call -t 4 -v -m -V indels -O z -o filtered.SNPs.vcf.gz AS.merged.bcf; Date=Sat May 22 18:32:35 2021                                  
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  AS.merged.bam

I'm not sure what has gone wrong here. Do I have to run the mpileup again with the --skip-variants indels flag?


bcftools


SNPs

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