User:Timothee Flutre/Notebook/Postdoc/2013/12/01: Difference between revisions

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(→‎One-liners for high-throughput sequencing data: add non-primary + link to SAM bits + reorder)
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     samtools view $OUT | cut -f2 | sort | uniq -c | sort -k1,1nr -k2,2n
     samtools view $OUT | cut -f2 | sort | uniq -c | sort -k1,1nr -k2,2n
    # | awk '{sum+=$1}END{print sum}' # <- same as line 1


[http://www.htslib.org/doc/sam.html list] of bits used to form the flags
[http://www.htslib.org/doc/sam.html list] of bits used to form the flags

Revision as of 07:17, 1 July 2015

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One-liners for high-throughput sequencing data

  • softwares: see BWA, Bowtie, MOSAIK, etc; they take fastq files as input and return bam files as output
   IN1="reads_R1.fastq.gz"
   IN2="reads_R2.fastq.gz"
   OUT="alignments.bam"
  • total number of reads in the fastq file:
   nbLines=$(zcat $IN1 | wc -l); echo "scale=0; "${nbLines}"/4" | bc -l
  • total number of reads in the bam file: should be equal to the nb of reads in the fastq file if no filtering was made
   samtools view $OUT | cut -f1 | sort | uniq | wc -l
  • flag statistics in SAM/BAM:
   samtools flagstat $OUT

which returns something like: 

   4635834 + 0 in total (QC-passed reads + QC-failed reads)
   20290 + 0 secondary
   0 + 0 supplimentary
   0 + 0 duplicates
   4443270 + 0 mapped (95.85%:-nan%)
   4615544 + 0 paired in sequencing
   2307772 + 0 read1
   2307772 + 0 read2
   4299122 + 0 properly paired (93.14%:-nan%)
   4412810 + 0 with itself and mate mapped
   10170 + 0 singletons (0.22%:-nan%)
   57898 + 0 with mate mapped to a different chr
   44330 + 0 with mate mapped to a different chr (mapQ>=5)
  • total number of entries in the bam file: same as line 1
   samtools view $OUT | wc -l
  • total number of mapped entries: same as line 5
   samtools view -F 0x4 $OUT | wc -l
  • total number of unmapped entries: same as line 1 - line 5
   samtools view -f 0x4 $OUT | wc -l
  • total number of non-primary entries: same as line 2
   samtools view -f 0x0100 $OUT | wc -l
  • list of different flags in the bam file: along with their number of occurrences
   samtools view $OUT | cut -f2 | sort | uniq -c | sort -k1,1nr -k2,2n
   # | awk '{sum+=$1}END{print sum}' # <- same as line 1

list of bits used to form the flags

this website is useful to interpret flags

for instance, if there are N entries with flag 99, there should also be N entries with flag 147; idem for 83 and 163; idem for 77 and 141; etc


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