I have used the samtools/bcftools/vcfutils pipeline to do variant calling.
step1:
samtools mpileup -uf reference.fa align-file1.bam align-file2.bam | bcftools view -bvcg >unfiltered-variants.bcf
step2:
bcftools view unfiltered-variants.bcf | vcfutils.pl varFilter -D100 >filtered-variants.vcf
This gives me about 30 variants in a format I can open in a spreadsheet.
However, I would also like to see the unfiltered variant list, so it needs to be in vcf format. I should be able to do this by changing the first step bcftools arguments to -vcg and the output file name to *.vcf. Actually this works up to certain point and I get partial output which matches the filtered variants, but it crashes at a certain line and I get sync error the number of fields does not match.
is there another way to just convert the bcf file into vcf to see all variants?
my other concern is that just about ALL variants found are indels. I have used IGV to look at the aligned contigs and I clearly see a number of SNPs.
I am trying to decipher the arguments it seems to me that the -c switch in bcftools should list SNPs?
I have seen a number of pages and read other posts, some of which are similar but just not quite the answer I need.
step1:
samtools mpileup -uf reference.fa align-file1.bam align-file2.bam | bcftools view -bvcg >unfiltered-variants.bcf
step2:
bcftools view unfiltered-variants.bcf | vcfutils.pl varFilter -D100 >filtered-variants.vcf
This gives me about 30 variants in a format I can open in a spreadsheet.
However, I would also like to see the unfiltered variant list, so it needs to be in vcf format. I should be able to do this by changing the first step bcftools arguments to -vcg and the output file name to *.vcf. Actually this works up to certain point and I get partial output which matches the filtered variants, but it crashes at a certain line and I get sync error the number of fields does not match.
is there another way to just convert the bcf file into vcf to see all variants?
my other concern is that just about ALL variants found are indels. I have used IGV to look at the aligned contigs and I clearly see a number of SNPs.
I am trying to decipher the arguments it seems to me that the -c switch in bcftools should list SNPs?
I have seen a number of pages and read other posts, some of which are similar but just not quite the answer I need.
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