I would like to print the alternative allele from a vcf file which i load in with htslib. The description of some functions: https://github.com/samtools/htslib/blob/develop/htslib/vcf.h

I have used bcf1_t objects by creating a header and reading the information.

htsFile *test_vcf = NULL;

  // creates header
  bcf_hdr_t *test_header = NULL;
  // initialize and allocate bcf1_t object
  bcf1_t *test_record = bcf_init();

  test_vcf = vcf_open("Testfile.vcf", "r");

  // returning a bcf_hdr_t struct 
  test_header = bcf_hdr_read(test_vcf);
  while(bcf_read(test_vcf, test_header, test_record) == 0){
    std::cout << "chr" << bcf_hdr_id2name(test_header, test_record->rid) << ":" <<test_record->pos+1 << std::endl;

But im not able to extract the reference or alternative allele information using this structure bcf1_t.

As far as i can read its perhaps possible with the structure and function:


But i am not able to get it to work since all the other functions seems limited to the bcf1_t struct.

Can anyone help with extracting the REF and ALT sequence? Thanks for your time


1 Answer 1


see the code in https://github.com/samtools/htslib/blob/develop/vcf.c#L3104

 bcf_unpack((bcf1_t*)v, BCF_UN_ALL);// if you need genotypes too, might use another constant to avoid decoding all the structure
 kputc('\t', s); // ALT
 if (v->n_allele > 1) {
        for (i = 1; i < v->n_allele; ++i) {
            if (i > 1) kputc(',', s);
            kputs(v->d.allele[i], s);
  • $\begingroup$ Thanks for reply, i'll try that!. $\endgroup$ Commented Nov 24, 2020 at 12:36
  • $\begingroup$ Okay, so as far as i understand based on this function, s is a kstring_t* which you can create using mem "kstring_t s = (kstring_t)&test_header->mem;", and then all the information is added to the pointer "s". But how are we then able to print or access the information in "s" ? I can see its a pointer declared with a reference, but then i should be able to print the values with *s. Again thanks for your time. $\endgroup$ Commented Nov 24, 2020 at 13:20
  • $\begingroup$ kstring_t is just the implementation of a dynamic string. you could just use ` cout << v->d.allele[i] << endl; ` $\endgroup$
    – Pierre
    Commented Nov 24, 2020 at 14:51
  • $\begingroup$ okay, that was my initial try, i just looked into it, and the problem is my n_allele for some reason is 0. So ill play around with it some more. Thanks again. $\endgroup$ Commented Nov 24, 2020 at 14:59

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