如何快速获取一个VCF中特定位点的信息

由于某些vcf文件比较大，检索感兴趣的位点，时间比较慢。尤其是当想批量获取位点信息时。
以下是一个linux 软件工具 或在python2脚本中导入该模块，提取某个位点的rs编号、深度等信息。

from cyvcf2 import VCF

for variant in VCF('some.vcf.gz'): # 输入vcf文件，然后就可以按照表头提取响应的值
    variant.REF, variant.ALT # e.g. REF='A', ALT=['C', 'T']

    variant.CHROM, variant.start, variant.end, variant.ID, \
                variant.FILTER, variant.QUAL

    # numpy arrays of specific things we pull from the sample fields.
    # gt_types is array of 0,1,2,3==HOM_REF, HET, UNKNOWN, HOM_ALT
    variant.gt_types, variant.gt_ref_depths, variant.gt_alt_depths # numpy arrays
    variant.gt_phases, variant.gt_quals, variant.gt_bases # numpy array

    ## INFO Field.
    ## extract from the info field by it's name:
    variant.INFO.get('DP') # int
    variant.INFO.get('FS') # float
    variant.INFO.get('AC') # float

    # convert back to a string.
    str(variant)


    ## sample info...

    # Get a numpy array of the depth per sample:
    dp = variant.format('DP')
    # or of any other format field:
    sb = variant.format('SB')
    assert sb.shape == (n_samples, 4) # 4-values per

# to do a region-query:

vcf = VCF('some.vcf.gz')
for v in vcf('11:435345-556565'):  #这里指我要提取11:435345-556565位置的信息
    if v.INFO["AF"] > 0.1: continue
    print(str(v))

下面的脚本是我想从dbsnp的vcf中提取，我感兴趣的位点rs编号和ref、alt碱基,

输入文件，argv[1]: dbsnp vcf文件； 第二个文件：argv[2] , 一些基因组位置表（chr，start...）
import sys
from cyvcf2 import VCF

dbsnp = VCF(sys.argv[1])
fp = open(sys.argv[2], "r")
for line in fp:
    lst = line.strip().split()
    chrom, st, rs, pro = lst[:]
    id = " "
    for v in dbsnp("%s:%s-%s" % (chrom, st, st)):
        id = v.ID
        print("%s\t%s\t%s\t%s" % (line.strip(), v.REF, v.ALT, id))
fp.close()

参考网址：cyvcf2