GATK Haplotype Caller error

Question

[kirti.amity]

While ruuning GATK Haplotype caller for human,

java -jar /biobank/seq/kirti/new/NA12878/GATK/GenomeAnalysisTK.jar -T HaplotypeCaller -R /biobank/seq/kirti/new/NA12878/reference/hg19_new.fa -I /biobank/seq/kirti/new/NA12878/nature_paper/"$a"/"$a"sorted2_bwa_aligned.bam --dbsnp /biobank/seq/kirti/new/NA12878/nature_paper/Homo_sapiens.vcf --sample_name "$a" -ploidy 2 -o /biobank/seq/kirti/new/NA12878/nature_paper/"$a"/"$a"bwa_GATK.vcf

I got this error message .Please help to solve it--Thanks in Advance--

<h5>ERROR MESSAGE: The provided VCF file is malformed at approximately line number 30824751: unparsable vcf record with allele W</h5>

Answer 1

[Pierre Lindenbaum]

the message is clear:

The provided VCF file is malformed at approximately line number 30824751: unparsable vcf record with allele W

there is an error in the REF or ALT column of your VCF, it should be an [ATGC] string but you have a 'W' allele.

thrown here: https://github.com/samtools/htsjdk/blob/912c28bec415c430b43515652ccaf13222b07e7b/src/main/java/htsjdk/variant/vcf/AbstractVCFCodec.java#L589

because of this line:

https://github.com/samtools/htsjdk/blob/912c28bec415c430b43515652ccaf13222b07e7b/src/main/java/htsjdk/variant/variantcontext/Allele.java#L338