Can we get the list of variants in the result?

[DhongiBoi]

After processing the VCF file we get a list of the number of variants, like how many variants were found in each chromosome. Can we get a list of those variants?

#Chr    Begin   End Size(Mb)    Nb_variants Percentage_homozygosity
chr1    41513572    44129738    2.62    58  89.66
chr1    86447582    89713973    3.27    42  90.48
chr2    128182225   130580573   2.40    27  88.89
chr3    38698526    42184659    3.49    36  91.67
chr4    81447479    88390810    6.94    48  95.83
chr5    139380057   146062570   6.68    85  89.41
chr5    146515817   148402169   1.89    29  93.10
chr6    46716485    47879229    1.16    37  94.59
chr11   47338502    49154505    1.82    26  88.46
chr15   51377428    55196867    3.82    40  92.50
chr19   18938389    22180787    3.24    42  95.24
chr22   27224553    35082493    7.86    81  93.83

So I want to know what are the 58 variants in chromosome 1. Is there a way we can get that?

[mquinodo]

Dear DhongiBoi,

This option is not available with AutoMap. However you can use other tools such as vcftools: vcftools --vcf input.vcf --bed region.bed --out output_prefix --recode --keep-INFO-all with region.bed containing your region, for example "chr1 41513572 44129738"

Best, Mathieu