$ cat r1.fq
@1
GGGCTAAGAGACAGCAAATACACATGAACAGAAAGAAGAGGGCAAAGAAAAGGCTGACGG
+
CCCFFFFFHHFHHJIJIJIJJJJJJJJDIJJJJJIJJIJJIIGIJJJJHIHJJJJIHIHI
$ cat r2.fq
@1
TAGTTTAAACGAGATTGCCAGGACCGGGTATCATTCACCATTTTTCTTTTCGTTAACTTG
+
CCCFFFFFHHHHHJJJIIIHIIJGGIGIJEIJIFGGGIJJJGFIIIJIFFEF?CFFEDCB
$ bwa mem ../ref/ref.fa r1.fq r2.fq > mem.sam;cat mem.sam
@SQ SN:1 LN:100000
@PG ID:bwa PN:bwa VN:0.7.10-r1017-dirty CL:bwa mem ../ref/ref.fa r1.fq r2.fq
1 81 1 1741 60 60M = 1681 -120 CCGTCAGCCTTTTCTTTGCCCTCTTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCC IHIHIJJJJHIHJJJJIGIIJJIJJIJJJJJIDJJJJJJJJIJIJIJHHFHHFFFFFCCC NM:i:1 MD:Z:18A41 AS:i:55 XS:i:0
1 161 1 1681 60 60M = 1741 120 TAGTTTAAACGAGATTGCCAGGACCGGGTATCATTCACCATTTTTCTTTTCGTTAACTTG CCCFFFFFHHHHHJJJIIIHIIJGGIGIJEIJIFGGGIJJJGFIIIJIFFEF?CFFEDCB NM:i:1 MD:Z:21C38 AS:i:55 XS:i:0
$ bwa aln ../ref/ref.fa r1.fq >r1.sai
$ bwa aln ../ref/ref.fa r2.fq >r2.sai
$ bwa sampe -r "@RG\tID:foo\tSM:bar" ../ref/ref.fa r1.sai r2.sai r1.fq r2.fq |\
samtools view -bS - > aln.bam
$ samtools view aln.bam
1 83 1 1741 60 60M = 1681 -120 CCGTCAGCCTTTTCTTTGCCCTCTTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCC IHIHIJJJJHIHJJJJIGIIJJIJJIJJJJJIDJJJJJJJJIJIJIJHHFHHFFFFFCCC RG:Z:foo XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:18A41
1 163 1 1681 60 60M = 1741 120 TAGTTTAAACGAGATTGCCAGGACCGGGTATCATTCACCATTTTTCTTTTCGTTAACTTG CCCFFFFFHHHHHJJJIIIHIIJGGIGIJEIJIFGGGIJJJGFIIIJIFFEF?CFFEDCB RG:Z:foo XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:21C38
the problem is:
samtools mpileup can't output valid results when the PROPER_PAIR flag not set.
@1
GGGCTAAGAGACAGCAAATACACATGAACAGAAAGAAGAGGGCAAAGAAAAGGCTGACGG
+
CCCFFFFFHHFHHJIJIJIJJJJJJJJDIJJJJJIJJIJJIIGIJJJJHIHJJJJIHIHI
$ cat r2.fq
@1
TAGTTTAAACGAGATTGCCAGGACCGGGTATCATTCACCATTTTTCTTTTCGTTAACTTG
+
CCCFFFFFHHHHHJJJIIIHIIJGGIGIJEIJIFGGGIJJJGFIIIJIFFEF?CFFEDCB
$ bwa mem ../ref/ref.fa r1.fq r2.fq > mem.sam;cat mem.sam
@SQ SN:1 LN:100000
@PG ID:bwa PN:bwa VN:0.7.10-r1017-dirty CL:bwa mem ../ref/ref.fa r1.fq r2.fq
1 81 1 1741 60 60M = 1681 -120 CCGTCAGCCTTTTCTTTGCCCTCTTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCC IHIHIJJJJHIHJJJJIGIIJJIJJIJJJJJIDJJJJJJJJIJIJIJHHFHHFFFFFCCC NM:i:1 MD:Z:18A41 AS:i:55 XS:i:0
1 161 1 1681 60 60M = 1741 120 TAGTTTAAACGAGATTGCCAGGACCGGGTATCATTCACCATTTTTCTTTTCGTTAACTTG CCCFFFFFHHHHHJJJIIIHIIJGGIGIJEIJIFGGGIJJJGFIIIJIFFEF?CFFEDCB NM:i:1 MD:Z:21C38 AS:i:55 XS:i:0
$ bwa aln ../ref/ref.fa r1.fq >r1.sai
$ bwa aln ../ref/ref.fa r2.fq >r2.sai
$ bwa sampe -r "@RG\tID:foo\tSM:bar" ../ref/ref.fa r1.sai r2.sai r1.fq r2.fq |\
samtools view -bS - > aln.bam
$ samtools view aln.bam
1 83 1 1741 60 60M = 1681 -120 CCGTCAGCCTTTTCTTTGCCCTCTTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCC IHIHIJJJJHIHJJJJIGIIJJIJJIJJJJJIDJJJJJJJJIJIJIJHHFHHFFFFFCCC RG:Z:foo XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:18A41
1 163 1 1681 60 60M = 1741 120 TAGTTTAAACGAGATTGCCAGGACCGGGTATCATTCACCATTTTTCTTTTCGTTAACTTG CCCFFFFFHHHHHJJJIIIHIIJGGIGIJEIJIFGGGIJJJGFIIIJIFFEF?CFFEDCB RG:Z:foo XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:21C38
the problem is:
samtools mpileup can't output valid results when the PROPER_PAIR flag not set.
Comment