Versions Compared

Old Version 3

changes.mady.by.user Daniel Edward Deatherage

Saved on

compared with

New Version 4

changes.mady.by.user Daniel Edward Deatherage

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

Code Block
languagebash
titleCalling variants using samtools and bcftools. Note the last command is quite long and may wrap around 2 lines your monitor or extend to the right of what you can see without scrolling over
linenumberstrue
mkdir samtools_example
cd samtools_example
samtools mpileup -u -f $SCRATCH/GVA_Human_trios/raw_files/ref/hs37d5.fa $SCRATCH/GVA_Human_trios/raw_files/NA12878.chrom20.ILLUMINA.bwa.CEU.exome.20111114.bam | bcftools call -v -c - > trios_tutorial.raw.vcf

The above command is expected to take ~3-5 minutes but may take >30 minutes to run based on some student's experience and will not produce many lines of output leading students to worry their terminal has locked up. More than likely this is not the case but get my attention on zoom if you think its been running for more than 5 minutes with no change in output, but you can try hitting the return key 1 or 2 times to see if your terminal adds a blank line to verify. As this command is taking so long it is recomended that you read ahead or switch to another tutorial in another terminal window while it runs, just be aware that you should not start 2 idev sessions in 2 different windows.

One potential issue with this type of approach is that vcf files only record variation that can be seen with the data provided. When all reads mapping to a given location exactly match the reference (i.e. is homozygous wildtype relative to the reference) there will be no data. Which looks the same as if you had no data in those regions; this leads us to our next topic. 

...