Dear Administators,
I used samtools software to call SNP my pooled samples (10-15 individuals), but
I'm not sure that obtained vcf files are correct, because I don't sure that
caller will be call minor allele to reference genome. Maybe I should use some
additional options? Or something else?
My command:
??samtools-1.6/samtools mpileup -Ou -f scaffolds.fasta -q 20 --rf 3 --ff 3844
*.bam | bcftools-1.6/bcftools call -m -Ov -o *.vcf
I will be very glad to any help in my problem.
________________________________
Sincerely, Nurislam Shaikhutdinov
Skolkovo Institute of Science and Technology
Skolkovo Innovation Center,
Building 3, Moscow,143026, Russia
Kazan (Volga region) Federal University
Department of Zoology and General Biology
Kremlevskaya str.18, Kazan, 420008, Russia
OpenLab "Extreme Biology"
Parizhskoy Kommuny str. 9, Kazan, 420021, Russia
Tel.: +7 (937) 281 82 95
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