Question: WARN in GATK HaplotypeCaller
11 months ago by
siyavash_damdar • 20
siyavash_damdar • 20 wrote:
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 ?
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