Wednesday, February 7, 2018

[bcf_sync] incorrect number of fields (0 != 5) at 0:0

The following samtools v0.1.18 mpileup command gave me error:

$ samtools mpileup -E -M0 -Q25 -q30 -m2 -D -S test_SortSam_withReadGroup.bam | bcftools view -vcg - > test.vcf
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
[bcf_sync] incorrect number of fields (0 != 5) at 0:0
[afs] 0:0.000

including option "-g" helped to overcome the problem.

$ samtools mpileup -g -E -M0 -Q25 -q30 -m2 -D -S test_S8_SortSam_withReadGroup.bam | bcftools view -vcg - > test.vcf

"-g " computes genotype likelihoods and output them in the binary call format (BCF).



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