Hi
I might be wrong but I got the impression that when using the c-option in the pileup process, then the read qualities are changed (near an indel, N's are placed also):
(I am using version 0.1.9 but version 0.1.10 seems to be the same). I am sure that there is an explanation, but I dont know it! Thanks for help!
Example: the differences are lines 68-71
with c option: (jump to line 67-75)
/apps/bi/samtools/c/samtools pileup -c test.bam -f test_ref.fa | less
test 67 A A 30 0 60 1 . 1
test 68 C N 0 0 0 1 . (
test 69 C N 0 0 0 1 . %
test 70 C N 0 0 0 1 . !
test 71 C N 0 0 0 1 .-1C !
test 71 * -C/-C 40 0 60 1 -C * 1 0 0 0 0
test 72 C N 0 0 0 1 * <
test 73 T T 30 0 60 1 . <
test 74 A A 30 0 60 1 . @
test 75 T T 30 0 60 1 . 1
without c option: (jump to line 67-75)
/apps/bi/samtools/c/samtools pileup test.bam -f test_ref.fa | less
test 67 A 1 . 1
test 68 C 1 . 1
test 69 C 1 . 1
test 70 C 1 . 1
test 71 C 1 .-1C 1
test 72 C 1 * <
test 73 T 1 . <
test 74 A 1 . @
test 75 T 1 . 1
Here is my test.sam file
@HD VN:0.0 GO:none SO:coordinate
@SQ SN:test LN:360
@PG ID:map2sam
GLXM4QB02GKAEH 0 test 1 255 71M1D17M1D20M1I147M * 0 0 GATCTCTTTTTCCAGTTTAAAAGTTCAGCTATTACAAGGTAAATGCAAAATGACAGTAAGGTTCCCACCCCTATTTTTCATCTTTTATGTCAAGAAGATACTTGTAAAAGAGAAGTAAGGTTAGGTATGATATTCGTTTATAAAGCATTTGGTGGAATACAGCGGTGGCAGGAAGTTGAACTGTCAACATTTTTGACCGTGTCAATTCATTTAATACATGTAGCCTGTATCTATTGAGTATATGGTACACATGCGG BAAABB55733>><94444444=99??>??<888?<<<89333=996666ABA???CDBAAAA<<;11111<@11100=?A?44444/4894443<98===993/.,,,-,559531266><866669:<<32444339@9;;<BBB???::8AAAA???DDDDDBBA?>===83../..33:8:9921,,,,,..--558875555:3...222679::9:32449898<<<<=AAAA@@<84449:666<::--
Here is the test_ref.fa file
>test
GATCTCTTTTTCCAGTTTAAAAGTTCAGCTATTACAAGGTAAATGCAAAATGACAGTAAG
GTTCCCACCCCCTATTTTTCATCTTTTATTGTCAAGAAGATACTTGCAAAGAGAAGTAAG
GTTAGGTATGATATTCGTTTATAAAGCATTTGGTGGAATACAGCGGTGGCAGGAAGTTGA
ACTGTCAACATTTTGTACCGTGTCAATTCATTTAATACATGTAGCCTGTATCTATTGAGT
ATATGGTACACATGCGGAAGTGTTCTGAGGATAAAGTCACGAAAAAAAAAAGGCACAATT
CTTGTTTTCAGGGAGATTATGTTCTAGTGAGGAGAATAATAGAAGAAGAAAGTCCCACTC
I might be wrong but I got the impression that when using the c-option in the pileup process, then the read qualities are changed (near an indel, N's are placed also):
(I am using version 0.1.9 but version 0.1.10 seems to be the same). I am sure that there is an explanation, but I dont know it! Thanks for help!
Example: the differences are lines 68-71
with c option: (jump to line 67-75)
/apps/bi/samtools/c/samtools pileup -c test.bam -f test_ref.fa | less
test 67 A A 30 0 60 1 . 1
test 68 C N 0 0 0 1 . (
test 69 C N 0 0 0 1 . %
test 70 C N 0 0 0 1 . !
test 71 C N 0 0 0 1 .-1C !
test 71 * -C/-C 40 0 60 1 -C * 1 0 0 0 0
test 72 C N 0 0 0 1 * <
test 73 T T 30 0 60 1 . <
test 74 A A 30 0 60 1 . @
test 75 T T 30 0 60 1 . 1
without c option: (jump to line 67-75)
/apps/bi/samtools/c/samtools pileup test.bam -f test_ref.fa | less
test 67 A 1 . 1
test 68 C 1 . 1
test 69 C 1 . 1
test 70 C 1 . 1
test 71 C 1 .-1C 1
test 72 C 1 * <
test 73 T 1 . <
test 74 A 1 . @
test 75 T 1 . 1
Here is my test.sam file
@HD VN:0.0 GO:none SO:coordinate
@SQ SN:test LN:360
@PG ID:map2sam
GLXM4QB02GKAEH 0 test 1 255 71M1D17M1D20M1I147M * 0 0 GATCTCTTTTTCCAGTTTAAAAGTTCAGCTATTACAAGGTAAATGCAAAATGACAGTAAGGTTCCCACCCCTATTTTTCATCTTTTATGTCAAGAAGATACTTGTAAAAGAGAAGTAAGGTTAGGTATGATATTCGTTTATAAAGCATTTGGTGGAATACAGCGGTGGCAGGAAGTTGAACTGTCAACATTTTTGACCGTGTCAATTCATTTAATACATGTAGCCTGTATCTATTGAGTATATGGTACACATGCGG BAAABB55733>><94444444=99??>??<888?<<<89333=996666ABA???CDBAAAA<<;11111<@11100=?A?44444/4894443<98===993/.,,,-,559531266><866669:<<32444339@9;;<BBB???::8AAAA???DDDDDBBA?>===83../..33:8:9921,,,,,..--558875555:3...222679::9:32449898<<<<=AAAA@@<84449:666<::--
Here is the test_ref.fa file
>test
GATCTCTTTTTCCAGTTTAAAAGTTCAGCTATTACAAGGTAAATGCAAAATGACAGTAAG
GTTCCCACCCCCTATTTTTCATCTTTTATTGTCAAGAAGATACTTGCAAAGAGAAGTAAG
GTTAGGTATGATATTCGTTTATAAAGCATTTGGTGGAATACAGCGGTGGCAGGAAGTTGA
ACTGTCAACATTTTGTACCGTGTCAATTCATTTAATACATGTAGCCTGTATCTATTGAGT
ATATGGTACACATGCGGAAGTGTTCTGAGGATAAAGTCACGAAAAAAAAAAGGCACAATT
CTTGTTTTCAGGGAGATTATGTTCTAGTGAGGAGAATAATAGAAGAAGAAAGTCCCACTC
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