Hello
by using bcftools calling, I want to list all the variants, including snp and indls. Any variant without filtering, even if there is only one snp or ind in a read .
Hello
by using bcftools calling, I want to list all the variants, including snp and indls. Any variant without filtering, even if there is only one snp or ind in a read .
You can try by first modifying --pval-threshold
, as I do here in this [now very old] pipeline: https://github.com/kevinblighe/ClinicalGradeDNAseq/blob/master/AnalysisMasterVersion1.sh#L282-L299
Note, also, the later filter step involving vcfutils.pl
: https://github.com/kevinblighe/ClinicalGradeDNAseq/blob/master/AnalysisMasterVersion1.sh#L372-L375
[vcfutils.pl
is an executable Perl script that comes bundled with BCFtools - check the [BCFTOOLS ROOT]/misc/
directory]
You may try piping BCFtools mpileup into vcfutils in order to reduce even further the thresholds, but not sure if it directly accepts pileup format.
Keep in mind that NGS is an inherently noisy technology and unsuitable for clinical applications without rigorous quality control mechanisms - a very large proportion of reads will contain variant bases due to this inherent 'noise', and other problems introduced by the downstream informatics programs, such as the aligner.
Kevin
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