Question: WARN in GATK HaplotypeCaller
0
gravatar for Siavash Salek Ardestani
2.8 years ago by

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 ?

snp gatk haplotypecaller • 926 views
ADD COMMENTlink modified 12 days ago by Biostar ♦♦ 20 • written 2.8 years ago by Siavash Salek Ardestani20
2
gravatar for _r_am
2.8 years ago by
_r_am32k
Baylor College of Medicine, Houston, TX
_r_am32k wrote:

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

ADD COMMENTlink written 2.8 years ago by _r_am32k

thank you so much, Mr.Ram.

ADD REPLYlink written 2.8 years ago by Siavash Salek Ardestani20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2185 users visited in the last hour
_