只是警告信息,没有看到报错;
可能你的过滤条件太严没有结果了;你降低过滤条件,看看有没有结果吧;
这是我运行的命令
vcftools --gzvcf all.varFilter.vcf.gz --recode --recode-INFO-all --stdout \
--maf 0.05 --max-missing 0.7 --minDP 4 --maxDP 1000 \
--minQ 30 --minGQ 80 --min-alleles 2 --max-alleles 2 |gzip - > all.clean.vcf.gz
这是我的报错
sing zlib version: 1.2.7
Warning: Expected at least 2 parts in FORMAT entry: ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another; will always be heterozygous and is not intended to describe called alleles">
Warning: Expected at least 2 parts in FORMAT entry: ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
Warning: Expected at least 2 parts in FORMAT entry: ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
Warning: Expected at least 2 parts in INFO entry: ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
Warning: Expected at least 2 parts in INFO entry: ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
Warning: Expected at least 2 parts in INFO entry: ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
Warning: Expected at least 2 parts in INFO entry: ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
Warning: Expected at least 2 parts in INFO entry: ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
Warning: Expected at least 2 parts in INFO entry: ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
Warning: Expected at least 2 parts in INFO entry: ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
Warning: Expected at least 2 parts in INFO entry: ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
After filtering, kept 132 out of 132 Individuals
Outputting VCF file...
After filtering, kept 0 out of a possible 144323059 Sites
No data left for analysis!
Run Time = 2247.00 seconds
INFO: Cleaning up image...