SNPs in samtools mpileup using multisample and individual samples
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?
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Devon Ryan
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int11ap1
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int11ap1
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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).
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it's stupid but you can use -m to call low coverage variant