Entering edit mode
4.1 years ago
Ric
▴
440
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