gravatar for Ric

2 hours ago by

Australia

Hi, I put the following SNP pipeline together:

samtools faidx split-assembly/1.fa
samtools mpileup -C 50 -Q 30 -f split-assembly/1.fa split-data/1.bam > BCF2-1.bcf

bcftools view BCF2-1.bcf 
vcfutils.pl varFilter -Q 0 BCF2-1.bcf > BCF2-1-snps.vcf

Unfortunately, I got the following error:

[mpileup] 2 samples in 1 input files
Failed to read from BCF2-1.bcf: unknown file type
Use of uninitialized value $t[7] in pattern match (m//) at /work/miniconda2/envs/samtools-snp/bin/vcfutils.pl line 295, <> line 1.
Use of uninitialized value $t[7] in pattern match (m//) at /work/miniconda2/envs/samtools-snp/bin/vcfutils.pl line 299, <> line 1.
Use of uninitialized value $t[7] in pattern match (m//) at /work/miniconda2/envs/samtools-snp/bin/vcfutils.pl line 302, <> line 1.
Use of uninitialized value $t[7] in pattern match (m//) at /work/miniconda2/envs/samtools-snp/bin/vcfutils.pl line 317, <> line 1.

What did I miss?

Thank you in advance



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