WARN in GATK HaplotypeCaller

Question

[Siavash Salek Ardestani]

Hi to all I ran this command:

java -Xmx16g -jar  /mnt/unison/home/ymiar/siavash/GenomeAnalysisTK-3.8-0-ge9d806836/GenomeAnalysisTK.jar \
  -R dna.toplevel.fa -T HaplotypeCaller -I samp1 -I samp2 -I samp3 \
  -o tothap.raw.snps.indels.g.vcf

and after running I have many same this log :

12:59:52,305 HaplotypeCallerGenotypingEngine - location 1:28628586-28628588: too many alternative alleles found (11) larger than the maximum requested with -maxAltAlleles (6), the following will be dropped: TCACACACACA, TCTCTCACACA, TCTCTCACACACACA, TCTCACACACACA, T.

Is it important in snp discovery? Is it possible make errors ?

Answer 1

[Ram]

No, it's just a warning. 6 is a good number to cap your ALT alleles at. It won't be a problem.

[Siavash Salek Ardestani]

thank you so much, Mr.Ram.