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baoxingsong / AnchorWave

Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism and whole-genome duplication variation
MIT License
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Error: could not parse the input VCF #56

Open wangzhx36 opened 11 months ago

wangzhx36 commented 11 months ago

Hi, Dr. Song I successfully generated alignment.maf using AnchorWave and converted it into a BAM file using the provided script. However, when I attempted to convert the BAM file to a VCF file using bcftools, I noticed that the output VCF file only contains partial variant information from the first chromosome. Below are my scripts and error messages. I'm not sure what the reason is, and I hope to get your assistance.

script: maf2bam=/data/software/AnchorWave-1.2.1/scripts/maf-convert sP1=/data2/projects/zwang/macropodus_compare/synteny/pseudogenome/Anchorwave/MOP/ sP2=/data2/projects/zwang/macropodus_compare/synteny/pseudogenome/Anchorwave/MOP/Betta_splendens python2 $maf2bam sam $sP2/alignment.maf | sed 's/[0-9]+H//g' \ | samtools view -O BAM --reference $sP1/mopscf1-23.fa - | samtools sort - > ./Bspl.bam samtools index $sP2/Bspl.bam bcftools mpileup -Ou -q 30 -f $sP1/mopscf1-23.fa $sP2/Bspl.cram | bcftools call -m -Ou | bcftools norm -f $sP1/mopscf1-23.fa -Oz -o Bspl.g.vcf.gz

error: [mpileup] 1 samples in 1 input files Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid [mpileup] maximum number of reads per input file set to -d 250 Error: could not parse the input VCF Lines total/split/realigned/skipped: 11397420/0/0/0

baoxingsong commented 11 months ago

We never succeeded in calling variants from AnchorWave alignments using any short-reads mapping variant calling pipeline. Please try this pipeline https://github.com/baoxingsong/AnchorWave/blob/master/doc/GATK.md