Update vcf header

Author: zhengzhenxian

shared/utils.py

@@ -281,7 +281,7 @@ def get_header(reference_file_path=None, cmd_fn=None, sample_name="SAMPLE", vers
             ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
             ##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
             ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
-            ##FORMAT=<ID=AF,Number=G,Type=Float,Description="Observed allele frequency in reads, for each ALT allele, in the same order as listed, or the REF allele for a RefCall">\n""".format(
+            ##FORMAT=<ID=AF,Number=A,Type=Float,Description="Observed allele frequency in reads, for each ALT allele, in the same order as listed, or the REF allele for a RefCall">\n""".format(
             version))
     else:
         header = dedent("""\
@@ -298,7 +298,7 @@ def get_header(reference_file_path=None, cmd_fn=None, sample_name="SAMPLE", vers
             ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads 1. with MQ below 5 or an user-specified threshold, or 2. selected by 'samtools view -F 2316', are filtered)">
             ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
             ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
-            ##FORMAT=<ID=AF,Number=G,Type=Float,Description="Observed allele frequency in reads, for each ALT allele, in the same order as listed, or the REF allele for a RefCall">\n""".format(
+            ##FORMAT=<ID=AF,Number=A,Type=Float,Description="Observed allele frequency in reads, for each ALT allele, in the same order as listed, or the REF allele for a RefCall">\n""".format(
             version))
     if ref_header_str != "":
         header_list = header.rstrip('\n').split('\n')