bcftools cannot switch alt and ref alleles, IDs missing

Question

[dec986]

Following advice from Switch ref/alt alleles vcf file

I am attempting to switch alt and ref alleles in a file with 659,535 sites.

I am running thus, as suggested by the tool itself:

bcftools +fixref vcf/HG00101.bb.include_variants.vcf.gz -Ob -o tmp.vcf.gz -- -f human_g1k_v37.fasta -i IM.NA19900.SM.vcf.gz

and the output is

# SC, guessed strand convention
SC  TOP-compatible  1
SC  BOT-compatible  1
# ST, substitution types
ST  A>C 0   -nan%
ST  A>G 0   -nan%
ST  A>T 0   -nan%
ST  C>A 0   -nan%
ST  C>G 0   -nan%
ST  C>T 0   -nan%
ST  G>A 0   -nan%
ST  G>C 0   -nan%
ST  G>T 0   -nan%
ST  T>A 0   -nan%
ST  T>C 0   -nan%
ST  T>G 0   -nan%
# NS, Number of sites:
NS  total           659352
NS  ref match       0   -nan%
NS  ref mismatch    0   -nan%
NS  flipped         0   -nan%
NS  swapped         0   -nan%
NS  flip+swap       0   -nan%
NS  unresolved      0   -nan%
NS  fixed pos       0   -nan%
NS  skipped         659352
NS  non-ACGT        0
NS  non-SNP         659352
NS  non-biallelic   0

so almost every site is skipped, why?

but the output bcf tmp.vcf is displaying the exact same data that I entered in, the alternate alleles and IDs are missing.

how can I run bcftools to add the alternate alleles and IDs according to IM.NA19900.SM.vcf.gz?

[Pierre Lindenbaum]

so almost every site is skipped, why?

to both input vcf files use the same notation for the chromosomes : 'chr1' vs '1' ?

[dec986]

the chromosomes all match

[Kevin Blighe]

I thought that you can do this with bcftools norm and the following option:

-c, --check-ref <e|w|x|s>         check REF alleles and exit (e), warn (w), exclude (x), or set (s) bad sites [e]

[dec986]

unfortunately, this still keep things in gVCF format :(