Samtools running time

Question

[botelho.amn]

Hi, guys!

I need some help. I am new using bioinformatics tools, I have no idea of what I am doing. I found a tutorial online that helped me to use Samtools for SNP calling using a bacterial whole genome. I followed the steps and everything went perfectly. But the last step is running for 12 hours now. Is it right? I don't have a clue, 'cause I never did it before. If anyone could tell me if I should wait or kill the process, it would be great!

Thank you!

[Devon Ryan]

What's the command you're using for the last step (please also post how you arrived at the input).

[botelho.amn]

These were all the commands I used, since the beginning of the process

bwa index -a bwtsw TW20.fasta
bwa aln TW20.fasta BMB9393.fasta > TW20_BMB9393-bwa.sai
bwa samse TW20.fasta TW20_BMB9393-bwa.sai BMB9393.fasta > TW20_BMB9393.sam
samtools view -S -ub TW20_BMB9393.sam | samtools sort - TW20_BMB9393
samtools index TW20_BMB9393.bam
samtools faidx TW20.fasta
samtools mpileup -g -f TW20.fasta TW20_BMB9393.bam > TW20_BMB9393-raw.bcf
bcftools view -bvcg TW20_BMB9393-raw.bcf > TW20_BMB9393.bcf
bcftools view TW20_BMB9393.bcf | less
/usr/share/samtools/vcfutils.pl varFilter - >> TW20_BMB9393.vcf

Answer 1

[Devon Ryan]

The last command will never complete. It's waiting for you to pipe input into it but you're not doing that. you want:

bcftools view TW20_BMB9393.bcf | /usr/share/samtools/vcfutils.pl varFilter someoptions > TW20_BMB9393.vcf

If you don't want to filter the VCF, then just don't pipe to vcfutils.pl and instead redirect the output to a file ( ... > file.vcf).

[botelho.amn]

Much better now! Thank you very much!