SNPs in samtools mpileup using multisample and individual samples

Question

[int11ap1]

I have the following SNP by calling variants using three samples at a time:

A4.TRINITY_DN6816_c0_g1_i1    76    .    G    A    3.19779    .    DP=13;VDB=0.160409;SGB=-7.43374;RPB=0.180092;MQB=1;MQSB=1;BQB=0.928296;MQ0F=0;AF1=0.478853;G3=1.80038e-07,1,1.18071e-20;HWE=0.0481583;AC1=3;DP4=7,2,4,0;MQ=20;FQ=4.83572;PV4=1,0.280723,1,0.0350635    GT:PL:DP:GQ    0/1:8,0,44:4:7    0/1:11,0,28:3:9    0/1:19,0,53:6:17

Why this variant does not appear by calling variants individually, if I see enough coverage at the individual samples to call it?

[stolarek.ir]

it's stupid but you can use -m to call low coverage variant

Answer 1

[Devon Ryan]

You have more power with more samples, so although you think there's enough power to call it on a single sample, samtools apparently disagrees (unsurprisingly given the low per-sample depth).