Greetings. I am using BWA to map reads from the Illumina 1.5 pipeline to contigs made with velvet and using SAMtools to call variants.
Looking in a genome browser, the .bam is perfect, and I can see nice SNPs, and just right amount as I would expect. But the VCFs come out empty.
When I look at the raw BCF/VCF with all the positions (not just variants) there are only 34 positions from the middle of one contig (somewhere in the middle of the reference file) and no variants, rather than the 951462 positions that should be there with plenty of variants.
It looks like this:
The coverage here is also ridiculously low, most positions are closer to 50-100X.
I have had the problem before when the fasta index (.fai) file was not made properly, but this time it's perfect.
What could be going on here?
Code:
samtools mpileup -uf contigs_ref.fasta Sample_to_contigs_rmdup.bam | bcftools view -bvcg -> Sample_to_contigs_rmdup.bam.bcf bcftools view Sample_to_contigs_rmdup.bam.bcf | vcfutils.pl varFilter >Sample_to_contigs_rmdup.bam.vcf
When I look at the raw BCF/VCF with all the positions (not just variants) there are only 34 positions from the middle of one contig (somewhere in the middle of the reference file) and no variants, rather than the 951462 positions that should be there with plenty of variants.
It looks like this:
Code:
##CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample_to_contigs_rmdup.bam Contig_14090_length_986 852 . A . 35.9 . DP=2;AF1=0;AC1=0;DP4=2,0,0,0;MQ=14;FQ=-33 PL 0 Contig_14090_length_986 853 . T . 32.9 . DP=3;AF1=0;AC1=0;DP4=2,0,1,0;MQ=12;FQ=-30.1;PV4=1,1,0.33,1 PL 0 Contig_14090_length_986 854 . A . 32.9 . DP=4;VDB=0.0768;AF1=0;AC1=0;DP4=2,0,1,0;MQ=12;FQ=-30.1;PV4=1,1,0.33,0 PL 0 Contig_14090_length_986 855 . T . 17.3 . DP=8;VDB=0.0004;AF1=0.6089;AC1=1;DP4=0,2,3,0;MQ=11;FQ=-23.6;PV4=0.1,1,0.47,1 PL 12 Contig_14090_length_986 856 . T . 48 . DP=11;AF1=0;AC1=0;DP4=4,2,0,0;MQ=13;FQ=-45 PL 0 Contig_14090_length_986 857 . A . 48 . DP=14;AF1=0;AC1=0;DP4=4,2,0,0;MQ=13;FQ=-45 PL 0 Contig_14090_length_986 858 . T . 48 . DP=15;AF1=0;AC1=0;DP4=4,2,0,0;MQ=13;FQ=-45 PL 0 Contig_14090_length_986 859 . A . 48 . DP=17;AF1=0;AC1=0;DP4=4,2,0,0;MQ=13;FQ=-45 PL 0 Contig_14090_length_986 860 . T . 48 . DP=18;AF1=0;AC1=0;DP4=4,2,0,0;MQ=13;FQ=-45 PL 0 Contig_14090_length_986 861 . A . 45 . DP=19;AF1=0;AC1=0;DP4=4,1,0,0;MQ=14;FQ=-42 PL 0 Contig_14090_length_986 862 . T . 42 . DP=19;AF1=0;AC1=0;DP4=4,0,0,0;MQ=14;FQ=-39 PL 0 Contig_14090_length_986 863 . A . 42 . DP=19;AF1=0;AC1=0;DP4=4,0,0,0;MQ=14;FQ=-39 PL 0 Contig_14090_length_986 864 . T . 42 . DP=19;AF1=0;AC1=0;DP4=4,0,0,0;MQ=14;FQ=-39 PL 0 Contig_14090_length_986 865 . A . 42 . DP=19;AF1=0;AC1=0;DP4=4,0,0,0;MQ=14;FQ=-39 PL 0 Contig_14090_length_986 866 . T . 42 . DP=19;AF1=0;AC1=0;DP4=4,0,0,0;MQ=14;FQ=-39 PL 0 Contig_14090_length_986 867 . A . 42 . DP=19;AF1=0;AC1=0;DP4=4,0,0,0;MQ=14;FQ=-39 PL 0 Contig_14090_length_986 868 . T . 42 . DP=19;AF1=0;AC1=0;DP4=4,0,0,0;MQ=14;FQ=-39 PL 0 Contig_14090_length_986 869 . A . 42 . DP=19;AF1=0;AC1=0;DP4=4,0,0,0;MQ=14;FQ=-39 PL 0 Contig_14090_length_986 870 . T . 42 . DP=19;AF1=0;AC1=0;DP4=4,0,0,0;MQ=14;FQ=-39 PL 0 Contig_14090_length_986 871 . A . 42 . DP=19;AF1=0;AC1=0;DP4=4,0,0,0;MQ=14;FQ=-39 PL 0 Contig_14090_length_986 872 . T . 42 . DP=19;AF1=0;AC1=0;DP4=4,0,0,0;MQ=14;FQ=-39 PL 0 Contig_14090_length_986 873 . A . 42 . DP=19;AF1=0;AC1=0;DP4=4,0,0,0;MQ=14;FQ=-39 PL 0 Contig_14090_length_986 874 . T . 42 . DP=19;AF1=0;AC1=0;DP4=4,0,0,0;MQ=14;FQ=-39 PL 0 Contig_14090_length_986 875 . A . 42 . DP=19;AF1=0;AC1=0;DP4=4,0,0,0;MQ=14;FQ=-39 PL 0 Contig_14090_length_986 876 . T . 42 . DP=19;AF1=0;AC1=0;DP4=4,0,0,0;MQ=14;FQ=-39 PL 0 Contig_14090_length_986 877 . A . 35.9 . DP=16;AF1=0;AC1=0;DP4=2,0,0,0;MQ=14;FQ=-33 PL 0 Contig_14090_length_986 878 . A . 10.4 . DP=15;VDB=0.0015;AF1=1;AC1=2;DP4=0,0,1,0;MQ=20;FQ=-30 PL 20 Contig_14090_length_986 879 . A . 33 . DP=15;AF1=0;AC1=0;DP4=1,0,0,0;MQ=20;FQ=-30 PL 0 Contig_14090_length_986 880 . T . 33 . DP=14;AF1=0;AC1=0;DP4=1,0,0,0;MQ=20;FQ=-30 PL 0 Contig_14090_length_986 881 . A . 33 . DP=13;AF1=0;AC1=0;DP4=1,0,0,0;MQ=20;FQ=-30 PL 0 Contig_14090_length_986 882 . T . 33 . DP=9;AF1=0;AC1=0;DP4=1,0,0,0;MQ=20;FQ=-30 PL 0 Contig_14090_length_986 883 . T . 28.2 . DP=6;VDB=0.0300;;AC1=2;FQ=-30 PL 0 Contig_14090_length_986 884 . A . 28.2 . DP=4;;AC1=2;FQ=-30 PL 0 Contig_14090_length_986 885 . A . 28.2 . DP=1;;AC1=2;FQ=-30 PL 0
I have had the problem before when the fasta index (.fai) file was not made properly, but this time it's perfect.
What could be going on here?
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