Hello everyone,
It's me again
Since I have finally worked through where to apply the parametre -trimAlternates, now I got another question.
When I running FastaAlternateReferenceMaker, I got the error message below:

ERROR --

ERROR stack trace

java.lang.IllegalArgumentException: Illegal base [ ] seen in the allele
at htsjdk.variant.variantcontext.Allele.create(Allele.java:231)
at htsjdk.variant.variantcontext.Allele.create(Allele.java:355)
at org.broadinstitute.gatk.tools.walkers.fasta.FastaAlternateReferenceMaker.map(FastaAlternateReferenceMaker.java:170)
at org.broadinstitute.gatk.tools.walkers.fasta.FastaAlternateReferenceMaker.map(FastaAlternateReferenceMaker.java:96)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:98)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:323)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:123)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)

ERROR ------------------------------------------------------------------------------------------

ERROR A GATK RUNTIME ERROR has occurred (version 3.8-0-ge9d806836):

ERROR

ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.

ERROR If not, please post the error message, with stack trace, to the GATK forum.

ERROR Visit our website and forum for extensive documentation and answers to

ERROR commonly asked questions https://software.broadinstitute.org/gatk

ERROR

ERROR MESSAGE: Illegal base [ ] seen in the allele

ERROR ------------------------------------------------------------------------------------------

It seems not the indels that bring such error cause I try to use only snp data to run the same command line, while got stuck by the same message.
Here is my working steps:

1 java -Xmx4g -jar GenomeAnalysisTK.jar -T SelectVariants -R Melc_scaffolds.fasta -V variant.vcf -sn MD -trimAlternates -env -nt 4 -o MD.vcf

2 java -Xmx4g -jar GenomeAnalysisTK.jar -T FastaAlternateReferenceMaker -R Melc_scaffolds.fasta -V MD.vcf -o MD.fasta

Actually, what I try to do is to convert VCF file to single fasta files and then uses them to construct phylogenetic tree, so any kind suggestion for fast and convenient format transition is appreciated.
Thanks for your attentions.
caiyc