Entering edit mode
5.5 years ago
DVA
▴
630
Hello,
I am trying to understand an error when running "samtools view":
Line 6040, sequence length 67 vs 76 from CIGAR
Parse error at line 6040: CIGAR and sequence length are inconsistent
I went back to check line 6040 from sam file (generated by HISAT2):
NR500449:117:H7WMXX:2:11101:6188:2761 99 10 103287073 60 3S73M = 103287096 102 TGGCAAGAGTGAGATGGCACGCCACCTTCGGGAATACCAGGACTTGCTCAATGTCAAAAACATTGAG AAAAAE6AA/EE/E///EEE//AEEEE/E/////E6E/EE/E<E///E//<EEE//</E//<AE6EE/E/E/EEE/ AS:i:-3 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:73 YS:i:-12 YT:Z:CP NH:i:1
And lines corresponding to this alignment in R1 and R2 from fastq files:
@NR500449:117:H7WMXX:2:11101:6188:2761 1:N:0:3
TGGCAAGAGTGAGATGGCACGCCACCTTCGGGAATACCAGGACTTGCTCAATGTCAAAATGGCTCTTGACATTGAG
+
AAAAAE6AA/EE/E///EEE//AEEEE/E/////E6E/EE/E<E///E//<EEE//</E//<AE6EE/E/E/EEE/
@NR500449:117:H7WMXX:2:11101:6188:2761 2:N:0:3
TCCTGCAGTTTCCTGTAAGCTGCTATCTCAATGTCAAGAGACATTTTGACATTGAGAAAGTCCTGGTATTACCGAA
+
A/A/A/E///EAEEEEEE//EEE/EEEEEEEEAA//A<EE//EEE/EEA//6/AE//EA/<6/EE/E<AE////<E
Indeed the CIGAR string represents 76bps, same as the seq length from fastq, but the sam line has only 67bps. Any idea about why would this happen and how to deal with it? Thank you very much.
Thank you for the conformation. I will update this post once I hear from them.